microsatbed: seqrequester/src/seqrequester/summarize.C annotate

annotate seqrequester/src/seqrequester/summarize.C @ 1:1085e094cf5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty

author	fubar
date	Sat, 13 Jul 2024 12:39:06 +0000
parents
children

rev	line source
1 1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	1
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	2 /******************************************************************************
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	3 *
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	4 * This file is part of seqrequester, a tool for summarizing, extracting,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	5 * generating and modifying DNA sequences.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	6 *
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	7 * This software is based on:
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	8 * 'Canu' v2.0 (https://github.com/marbl/canu)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	9 * which is based on:
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	10 * 'Celera Assembler' r4587 (http://wgs-assembler.sourceforge.net)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	11 * the 'kmer package' r1994 (http://kmer.sourceforge.net)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	12 *
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	13 * Except as indicated otherwise, this is a 'United States Government Work',
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	14 * and is released in the public domain.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	15 *
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	16 * File 'README.licenses' in the root directory of this distribution
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	17 * contains full conditions and disclaimers.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	18 */
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	19
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	20 #include "seqrequester.H"
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	21
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	22 bool
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	23 summarizeParameters::parseOption(opMode &mode, int32 &arg, int32 argc, char **argv) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	24
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	25 if (strcmp(argv[arg], "summarize") == 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	26 mode = modeSummarize;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	27 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	28
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	29 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-size") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	30 genomeSize = strtoull(argv[++arg], nullptr, 10);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	31 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	32
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	33 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-1x") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	34 limitTo1x = true;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	35 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	36
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	37 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-split-n") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	38 breakAtN = true;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	39 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	40
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	41 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-simple") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	42 asSimple();
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	43 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	44
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	45 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-lengths") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	46 asLengths();
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	47 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	48
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	49 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-seqlen") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	50 asSeqLen();
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	51 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	52
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	53 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-assequences") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	54 asSequences = true;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	55 asBases = false;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	56 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	57
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	58 else if ((mode == modeSummarize) && (strcmp(argv[arg], "-asbases") == 0)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	59 asSequences = false;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	60 asBases = true;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	61 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	62
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	63 else {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	64 return(false);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	65 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	66
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	67 return(true);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	68 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	69
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	70
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	71
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	72 void
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	73 summarizeParameters::showUsage(opMode mode) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	74
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	75 if (mode != modeSummarize)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	76 return;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	77
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	78 fprintf(stderr, "OPTIONS for summarize mode:\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	79 fprintf(stderr, " -size base size to use for N50 statistics\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	80 fprintf(stderr, " -1x limit NG table to 1x coverage\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	81 fprintf(stderr, "\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	82 fprintf(stderr, " -split-n split sequences at N bases before computing length\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	83 fprintf(stderr, "\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	84 fprintf(stderr, " Output format:\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	85 fprintf(stderr, " (default) output an N50 table, a histogram picture and mono-,\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	86 fprintf(stderr, " di- and tri-nucleotide frequencies\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	87 fprintf(stderr, " -simple output a simple 'length numSequences' histogram\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	88 fprintf(stderr, " -lengths output a list of 'length' for each sequence\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	89 fprintf(stderr, " -seqlen output a list of 'length name' for each sequence\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	90 fprintf(stderr, "\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	91 fprintf(stderr, " -assequences load data as complete sequences (for testing)\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	92 fprintf(stderr, " -asbases load data as blocks of bases (for testing)\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	93 fprintf(stderr, "\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	94 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	95
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	96
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	97
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	98 bool
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	99 summarizeParameters::checkOptions(opMode mode, vector<char const > &inputs, vector<char const > &errors) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	100
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	101 if (mode != modeSummarize)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	102 return(false);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	103
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	104 if (inputs.size() == 0)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	105 sprintf(errors, "ERROR: No input sequence files supplied.\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	106
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	107 return(errors.size() > 0);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	108 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	109
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	110
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	111
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	112 bool
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	113 doSummarize_loadSequence(dnaSeqFile *sf,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	114 bool asSequences,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	115 char *&name, uint32 &nameMax,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	116 char *&seq,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	117 uint8 *&qlt, uint64 &seqMax,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	118 uint64 &seqLen) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	119 uint32 error = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	120
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	121 if (asSequences)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	122 return(sf->loadSequence(name, nameMax, seq, qlt, seqMax, seqLen, error));
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	123
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	124 // Otherwise, piece it together from multiple calls to get bases.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	125 // loadBases() returns true if bases were loaded, and sets endOfSeq
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	126 // if the block returned is to the end of a sequence.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	127
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	128 uint64 bufferMax = 23;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	129 uint64 bufferLen = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	130 char *buffer = new char [bufferMax];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	131 bool endOfSeq = false;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	132
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	133 merylutil::resizeArray(name, 0, nameMax, (uint32)1024);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	134 merylutil::resizeArrayPair(seq, qlt, 0, seqMax, seqLen+1);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	135
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	136 name[0] = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	137 seq[0] = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	138 qlt[0] = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	139
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	140 seqLen = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	141
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	142 while (sf->loadBases(buffer, bufferMax, bufferLen, endOfSeq)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	143 if (seqLen + bufferLen >= seqMax)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	144 merylutil::resizeArrayPair(seq, qlt, seqLen, seqMax, 2 * (seqLen + bufferLen + 1));
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	145
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	146 assert(seqLen + bufferLen + 1 < seqMax);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	147
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	148 memcpy(seq + seqLen, buffer, sizeof(char) * bufferLen);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	149 seqLen += bufferLen;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	150
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	151 seq[seqLen] = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	152
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	153 if (endOfSeq)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	154 break;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	155 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	156
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	157 // We get here in two ways:
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	158 // loadBases() immediately hit EOF, it will return false and set endOfSeq = false.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	159 // Otherwise, it found a sequence and endOfSeq (here) _must_ be true.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	160 // So, we can just return endOfSeq to mean 'there might be another sequence to load'.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	161
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	162 delete [] buffer;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	163
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	164 return(endOfSeq);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	165 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	166
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	167
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	168
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	169 void
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	170 doSummarize_lengthHistogramSimple(uint64 *shortLengths,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	171 uint32 shortLengthsLen,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	172 vector<uint64> &longLengths) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	173
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	174 // Short lengths are super easy; they're already a histogram.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	175
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	176 for (uint64 ll=0; ll<shortLengthsLen; ll++)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	177 if (shortLengths[ll] > 0)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	178 fprintf(stdout, "%lu\t%lu\n", ll, shortLengths[ll]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	179
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	180 // Long lengths need to be sorted then counted.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	181
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	182 sort(longLengths.begin(), longLengths.end(), less<uint64>());
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	183
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	184 for (uint64 bgn=0, end=1; bgn < longLengths.size(); bgn=end, end++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	185 while ((end < longLengths.size()) &&
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	186 (longLengths[bgn] == longLengths[end]))
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	187 end++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	188
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	189 fprintf(stdout, "%lu\t%lu\n", longLengths[bgn], end - bgn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	190 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	191 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	192
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	193
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	194
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	195 void
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	196 doSummarize_dumpLengths(uint64 *shortLengths,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	197 uint32 shortLengthsLen,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	198 vector<uint64> &longLengths) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	199
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	200 // Dump the shorter lengths.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	201
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	202 for (uint64 ll=0; ll<shortLengthsLen; ll++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	203 if (shortLengths[ll] == 0)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	204 continue;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	205
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	206 for (uint64 cc=0; cc<shortLengths[ll]; cc++)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	207 fprintf(stdout, "%lu\n", ll);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	208 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	209
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	210 // Dump the longer lengths.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	211
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	212 sort(longLengths.begin(), longLengths.end(), less<uint64>());
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	213
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	214 for (uint64 ii=0; ii<longLengths.size(); ii++)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	215 fprintf(stdout, "%lu\n", longLengths[ii]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	216 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	217
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	218
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	219
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	220 void
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	221 doSummarize_lengthHistogram(uint64 *shortLengths,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	222 uint32 shortLengthsLen,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	223 vector<uint64> &longLengths,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	224 uint64 genomeSize,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	225 bool limitTo1x) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	226
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	227 // NG table dimensions
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	228 uint32 nNG = 0; // Number of lines in the NG table.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	229
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	230 uint64 lSum = 0; // Sum of the lengths we've encountered so far
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	231
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	232 uint32 nStep = 10; // Step of each N report.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	233 uint32 nVal = nStep; // Index of the threshold we're next printing.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	234 uint64 nThr = genomeSize * nVal / 100; // Threshold lenth; if sum is bigger, emit and move to the next threshold
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	235
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	236 // These need to be sorted at some point, so might as well do it now.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	237 // Note! Sorted high to low.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	238
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	239 sort(longLengths.begin(), longLengths.end(), greater<uint64>());
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	240
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	241 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	242 // Find the minimum and maximum lengths, and count the number of
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	243 // non-zero-length sequences.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	244 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	245
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	246 uint64 minLength = uint64max;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	247 uint64 maxLength = uint64min;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	248 uint64 nSeqs = longLengths.size(); // Number of sequences we're summarizing.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	249
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	250 for (uint64 ll=0; ll<shortLengthsLen; ll++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	251 if (shortLengths[ll] > 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	252 minLength = std::min(minLength, ll);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	253 maxLength = std::max(maxLength, ll);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	254 nSeqs += shortLengths[ll];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	255 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	256 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	257
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	258 if (longLengths.size() > 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	259 minLength = std::min(minLength, longLengths.back());
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	260 maxLength = std::max(minLength, longLengths.front());
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	261 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	262
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	263 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	264 // Count the number of lines we expect to get in the NG table.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	265 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	266
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	267 auto setStep = [&]()
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	268 {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	269 while (lSum >= nThr) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	270 nNG++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	271
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	272 if (nVal < 200) nVal += nStep;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	273 else if (nVal < 2000) nVal += nStep * 10;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	274 else if (nVal < 20000) nVal += nStep * 100;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	275 else if (nVal < 200000) nVal += nStep * 1000;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	276 else nVal += nStep * 10000;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	277
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	278 nThr = genomeSize * nVal / 100;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	279 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	280 };
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	281
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	282 for (uint64 ll=0; ll<shortLengthsLen; ll++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	283 for (uint64 cc=0; cc<shortLengths[ll]; cc++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	284 lSum += ll;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	285 setStep();
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	286 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	287 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	288
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	289 for (uint64 ii=0; ii<longLengths.size(); ii++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	290 lSum += longLengths[ii];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	291 setStep();
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	292 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	293
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	294 if (nNG < 10)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	295 nNG = 10;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	296
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	297 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	298 // Decide how many rows to make in the length histogram table, and how
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	299 // many sequences each row will capture.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	300 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	301 // Set it to max(40, nNG) -- either a comfortable table or whatever the NG
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	302 // table is -- but reset to 1 sequence per row if it is too big.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	303 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	304
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	305 uint32 nLHcols = 63; // Magic number to make the histogram the same width as the trinucleotide list
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	306 uint32 nLH = 40; // Default height of the histogram; dynamically set below.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	307
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	308 uint32 bucketSize = (uint32)ceil((double)(maxLength - minLength) / std::max(nLH, nNG));
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	309
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	310 if (bucketSize == 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	311 nLH = 1;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	312 bucketSize = 1;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	313 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	314
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	315 nLH = 1 + (maxLength - minLength) / bucketSize; // With new bucketSize set, compute actual number of rows.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	316
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	317 if (lSum == 0)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	318 nLH = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	319
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	320 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	321 // Compute the length histogram.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	322 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	323
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	324 uint32 *nSeqPerLen = new uint32 [nLH];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	325
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	326 for (uint32 rr=0; rr<nLH; rr++) // Clear the histogram.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	327 nSeqPerLen[rr] = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	328
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	329 for (uint64 ll=0; ll<shortLengthsLen; ll++) { // Count the number of sequences per size range.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	330 if (shortLengths[ll] > 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	331 uint32 r = (ll - minLength) / bucketSize;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	332
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	333 assert(r < nLH);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	334 nSeqPerLen[r] += shortLengths[ll];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	335 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	336 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	337
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	338 for (uint64 ii=0; ii<longLengths.size(); ii++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	339 uint32 r = (longLengths[ii] - minLength) / bucketSize;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	340
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	341 assert(r < nLH);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	342 nSeqPerLen[r]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	343 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	344
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	345 // Find the maximum size of any bucket.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	346
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	347 uint64 maxCount = 1;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	348
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	349 for (uint32 rr=0; rr<nLH; rr++)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	350 if (maxCount < nSeqPerLen[rr])
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	351 maxCount = nSeqPerLen[rr];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	352
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	353 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	354 // Generate the length histogram table.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	355 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	356
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	357 lSum = 0; // Reset for actually generating the length histogram.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	358 nStep = 10;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	359 nVal = nStep;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	360 nThr = genomeSize * nVal / 100;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	361
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	362 // For each line in the histogram table, write the size range and draw a picture.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	363
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	364 char *histPlot = new char [nLH];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	365
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	366 for (uint32 rr=0; rr<nLH; rr++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	367 uint32 nn = (uint32)ceil(nSeqPerLen[rr] * nLHcols / (double)maxCount);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	368 uint64 lo = (rr+0) * bucketSize + minLength;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	369 uint64 hi = (rr+1) * bucketSize + minLength - 1;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	370
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	371 //fprintf(stdout, "rr %u bucketsize %u minLength %lu lo %lu hi %lu\n", rr, bucketSize, minLength, lo, hi);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	372
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	373 histPlot[rr] = new char [28 + nLHcols + 1]; // 28 = 9 + 1 + 9 + 1 + 7 + 1
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	374
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	375 if (lo == hi) // Size range and number of sequences.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	376 sprintf(histPlot[rr], "%9lu %7u\|",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	377 lo, nSeqPerLen[rr]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	378 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	379 sprintf(histPlot[rr], "%9lu-%-9lu %7u\|",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	380 lo, hi, nSeqPerLen[rr]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	381
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	382 for (uint32 cc=0; cc<nn; cc++) // ...histogram bars.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	383 histPlot[rr][28 + cc] = '-';
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	384
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	385 histPlot[rr][28 + nn] = 0; // ...terminate the line.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	386 //fprintf(stdout, "histplot'%s'\n", histPlot[rr]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	387 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	388
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	389 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	390 // Output N table, with length histogram appended at the end of each line.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	391 //
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	392 uint32 np = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	393 uint32 hp = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	394
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	395 fprintf(stdout, "\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	396 fprintf(stdout, "G=%-12lu" " sum of \|\| length num\n", genomeSize);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	397 fprintf(stdout, "NG length index lengths \|\| range seqs\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	398 fprintf(stdout, "----- ------------ --------- ------------ \|\| ------------------- -------\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	399
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	400 // Write lines if we're showing all data, or if we're below 1x coverage.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	401
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	402 auto emitLine = [&](uint64 seqlen, uint64 seqnum)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	403 {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	404 lSum += seqlen;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	405
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	406 while (lSum >= nThr) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	407 if ((limitTo1x == false) \|\|
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	408 (nVal <= 100)) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	409 if (hp < nLH)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	410 fprintf(stdout, "%05u %12lu %9lu %12lu \|\| %s\n", nVal, seqlen, seqnum, lSum, histPlot[hp++]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	411 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	412 fprintf(stdout, "%05u %12lu %9lu %12lu \|\|\n", nVal, seqlen, seqnum, lSum);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	413 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	414
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	415 if (nVal < 200) nVal += nStep;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	416 else if (nVal < 2000) nVal += nStep * 10;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	417 else if (nVal < 20000) nVal += nStep * 100;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	418 else if (nVal < 200000) nVal += nStep * 1000;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	419 else nVal += nStep * 10000;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	420
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	421 nThr = genomeSize * nVal / 100;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	422 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	423 };
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	424
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	425 uint64 ns = 1; // Sequences start at 1, not zero!
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	426
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	427 for (uint64 ii=0; ii<longLengths.size(); ii++, ns++)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	428 emitLine(longLengths[ii], ns);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	429
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	430 for (uint64 ll=shortLengthsLen; ll-- > 0; )
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	431 for (uint64 cc=0; cc<shortLengths[ll]; cc++, ns++)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	432 emitLine(ll, ns);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	433
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	434 assert(ns-1 == nSeqs);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	435
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	436 // Output up to 1x coverage regardless of how much is there.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	437
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	438 while (nVal <= 100) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	439 if (hp < nLH)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	440 fprintf(stdout, "%05" F_U32P " %12s %9s %12s \|\| %s\n",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	441 nVal, "-", "-", "-",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	442 histPlot[hp++]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	443 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	444 fprintf(stdout, "%05" F_U32P " %12s %9s %12s \|\|\n",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	445 nVal, "-", "-", "-");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	446
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	447 nVal += nStep;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	448 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	449
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	450 // If we're displaying exactly 1x, write empty lines to get to there.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	451 #if 0
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	452 if (limitTo1x == true) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	453 while (nVal <= 100) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	454 if (hp < nLH)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	455 fprintf(stdout, "%05" F_U32P " %12s %9s %12s \|\| %s\n",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	456 nVal, "-", "-", "-",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	457 histPlot[hp++]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	458 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	459 fprintf(stdout, "%05" F_U32P " %12s %9s %12s \|\|\n",
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	460 nVal, "-", "-", "-");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	461
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	462 nVal += nStep;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	463 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	464 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	465 #endif
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	466
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	467 // Now the summary line for the NG table.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	468
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	469 if (genomeSize == 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	470 if (hp < nLH)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	471 fprintf(stdout, "%07.3fx %9lu %12lu \|\| %s\n", 0.0, nSeqs, lSum, histPlot[hp++]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	472 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	473 fprintf(stdout, "%07.3fx %9lu %12lu \|\|\n", 0.0, nSeqs, lSum);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	474 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	475 else {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	476 if (hp < nLH)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	477 fprintf(stdout, "%07.3fx %9lu %12lu \|\| %s\n", (double)lSum / genomeSize, nSeqs, lSum, histPlot[hp++]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	478 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	479 fprintf(stdout, "%07.3fx %9lu %12lu \|\|\n", (double)lSum / genomeSize, nSeqs, lSum);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	480 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	481
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	482
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	483 // And any remaining length table lines.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	484
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	485 while (hp < nLH)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	486 fprintf(stdout, " \|\| %s\n", histPlot[hp++]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	487
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	488 fprintf(stdout, "\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	489
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	490 // Cleanup.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	491
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	492 for (uint32 rr=0; rr<nLH; rr++)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	493 delete [] histPlot[rr];
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	494
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	495 delete [] histPlot;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	496 delete [] nSeqPerLen;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	497 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	498
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	499
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	500
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	501 void
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	502 doSummarize(vector<char const *> &inputs,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	503 summarizeParameters &sumPar) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	504 uint32 shortLengthsLen = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	505 uint64 *shortLengths = nullptr;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	506 vector<uint64> longLengths;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	507
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	508 uint64 nBases = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	509
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	510 uint32 mer = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	511
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	512 uint64 mn[4] = {0};
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	513 uint64 dn[4*4] = {0};
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	514 uint64 tn[444] = {0};
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	515
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	516 double nmn = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	517 double ndn = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	518 double ntn = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	519
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	520 uint32 nameMax = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	521 char *name = nullptr;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	522 uint64 seqMax = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	523 char *seq = nullptr;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	524 uint8 *qlt = nullptr;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	525 uint64 seqLen = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	526
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	527 if (sumPar.isSeqLen()) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	528 fprintf(stdout, "--------- ------------ ----------------\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	529 fprintf(stdout, "-index length sequence-name\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	530 fprintf(stdout, "--------- ------------ ----------------\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	531 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	532
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	533 merylutil::allocateArray(shortLengths, shortLengthsLen, 1048576);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	534
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	535 for (uint32 ff=0; ff<inputs.size(); ff++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	536 dnaSeqFile *sf = openSequenceFile(inputs[ff]);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	537
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	538 // If sequence,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	539 // Count mono-, di- and tri-nucleotides.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	540 // Count number of mono-, di- and tri-nucleotides.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	541 // Count number of sequences and total bases.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	542 // Save the lengths of sequences.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	543
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	544 while (doSummarize_loadSequence(sf, sumPar.asSequences, name, nameMax, seq, qlt, seqMax, seqLen) == true) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	545 uint64 pos = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	546 uint64 bgn = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	547
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	548 if (pos < seqLen) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	549 mer = ((mer << 2) \| ((seq[pos++] >> 1) & 0x03)) & 0x3f;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	550 mn[mer & 0x03]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	551 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	552
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	553 if (pos < seqLen) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	554 mer = ((mer << 2) \| ((seq[pos++] >> 1) & 0x03)) & 0x3f;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	555 mn[mer & 0x03]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	556 dn[mer & 0x0f]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	557 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	558
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	559 while (pos < seqLen) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	560 mer = ((mer << 2) \| ((seq[pos++] >> 1) & 0x03)) & 0x3f;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	561 mn[mer & 0x03]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	562 dn[mer & 0x0f]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	563 tn[mer & 0x3f]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	564 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	565
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	566 nmn += (seqLen-0);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	567 ndn += (seqLen < 2) ? 0 : (seqLen-1);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	568 ntn += (seqLen < 3) ? 0 : (seqLen-2);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	569
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	570 // Report seq-len if requensted.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	571
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	572 if (sumPar.isSeqLen())
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	573 fprintf(stdout, "%-9lu %12lu %s\n", sf->seqIdx()+1, seqLen, name);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	574
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	575 // If we're NOT splitting on N, add one sequence of the given length.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	576
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	577 if (sumPar.breakAtN == false) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	578 nBases += seqLen;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	579
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	580 if (seqLen < shortLengthsLen)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	581 shortLengths[seqLen]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	582 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	583 longLengths.push_back(seqLen);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	584
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	585 continue;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	586 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	587
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	588 // But if we ARE splitting on N, add multiple sequences.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	589
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	590 pos = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	591 bgn = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	592
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	593 while (pos < seqLen) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	594 while ((pos < seqLen) && ((seq[pos] == 'n') \|\| // Skip N's.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	595 (seq[pos] == 'N')))
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	596 pos++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	597
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	598 bgn = pos; // Remember our start position.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	599
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	600 while ((pos < seqLen) && ((seq[pos] != 'n') && // Move ahead until the end of sequence or an N.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	601 (seq[pos] != 'N')))
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	602 pos++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	603
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	604 if (pos - bgn > 0) { // If a non-empty sequence
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	605 nBases += pos - bgn; // summarize it.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	606
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	607 if (pos - bgn < shortLengthsLen)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	608 shortLengths[pos - bgn]++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	609 else
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	610 longLengths.push_back(pos - bgn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	611 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	612 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	613 } // Over sequences in the file.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	614
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	615 delete sf;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	616 } // Over input files.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	617
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	618 delete [] name;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	619 delete [] seq;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	620 delete [] qlt;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	621
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	622 if (sumPar.genomeSize == 0) // If no genome size supplied, set it to the sum of lengths.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	623 sumPar.genomeSize = nBases;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	624
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	625 // If only a simple histogram of lengths is requested, dump and done.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	626
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	627 if (sumPar.isSimple() == true) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	628 doSummarize_lengthHistogramSimple(shortLengths, shortLengthsLen, longLengths);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	629 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	630
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	631 // If only the read lengths are requested, dump and done.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	632
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	633 else if (sumPar.isLengths() == true) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	634 doSummarize_dumpLengths(shortLengths, shortLengthsLen, longLengths);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	635 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	636
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	637 // Otherwise, generate a fancy histogram plot.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	638 // And finish with the mono-, di- and tri-nucleotide frequencies.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	639
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	640 else if (sumPar.isComplex() == true) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	641 doSummarize_lengthHistogram(shortLengths, shortLengthsLen, longLengths, sumPar.genomeSize, sumPar.limitTo1x);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	642
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	643 if (nmn == 0) nmn = 1; // Avoid divide by zero.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	644 if (ndn == 0) ndn = 1;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	645 if (ntn == 0) ntn = 1;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	646
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	647 double gc = 100.0 * (mn[0x01] + mn[0x03]) / nmn;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	648 double at = 100.0 * (mn[0x00] + mn[0x02]) / nmn;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	649
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	650 #define FMT "%12lu %6.4f"
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	651 #define GC "%05.02f%%"
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	652
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	653 char gcat[16] = { 0 };
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	654
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	655 if (gc >= 99.995) snprintf(gcat, 16, "100.0%% 00.00%%"); // What a bother! The default 5.2 format overflows
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	656 else if (at >= 99.995) snprintf(gcat, 16, "00.00%% 100.0%%"); // when the value is 100, and we're _forced_ to special
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	657 else snprintf(gcat, 16, "%05.02f%% %05.02f%%", gc, at); // case those two values.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	658
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	659 fprintf(stdout, "--------------------- --------------------- ----------------------------------------------------------------------------------------------\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	660 fprintf(stdout, " mononucleotide dinucleotide trinucleotide\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	661 fprintf(stdout, "--------------------- --------------------- ----------------------------------------------------------------------------------------------\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	662 fprintf(stdout, "" FMT " A" FMT " AA" FMT " AAA " FMT " AAC " FMT " AAG " FMT " AAT\n", mn[0x00], mn[0x00] / nmn, dn[0x00], dn[0x00] / ndn, tn[0x00], tn[0x00] / ntn, tn[0x01], tn[0x01] / ntn, tn[0x03], tn[0x03] / ntn, tn[0x02], tn[0x02] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	663 fprintf(stdout, "" FMT " C" FMT " AC" FMT " ACA " FMT " ACC " FMT " ACG " FMT " ACT\n", mn[0x01], mn[0x01] / nmn, dn[0x01], dn[0x01] / ndn, tn[0x04], tn[0x04] / ntn, tn[0x05], tn[0x05] / ntn, tn[0x07], tn[0x07] / ntn, tn[0x06], tn[0x06] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	664 fprintf(stdout, "" FMT " G" FMT " AG" FMT " AGA " FMT " AGC " FMT " AGG " FMT " AGT\n", mn[0x03], mn[0x03] / nmn, dn[0x03], dn[0x03] / ndn, tn[0x0c], tn[0x0c] / ntn, tn[0x0d], tn[0x0d] / ntn, tn[0x0f], tn[0x0f] / ntn, tn[0x0e], tn[0x0e] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	665 fprintf(stdout, "" FMT " T" FMT " AT" FMT " ATA " FMT " ATC " FMT " ATG " FMT " ATT\n", mn[0x02], mn[0x02] / nmn, dn[0x02], dn[0x02] / ndn, tn[0x08], tn[0x08] / ntn, tn[0x09], tn[0x09] / ntn, tn[0x0b], tn[0x0b] / ntn, tn[0x0a], tn[0x0a] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	666 fprintf(stdout, " " FMT " CA" FMT " CAA " FMT " CAC " FMT " CAG " FMT " CAT\n", dn[0x04], dn[0x04] / ndn, tn[0x10], tn[0x10] / ntn, tn[0x11], tn[0x11] / ntn, tn[0x13], tn[0x13] / ntn, tn[0x12], tn[0x12] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	667 fprintf(stdout, " --GC-- --AT-- " FMT " CC" FMT " CCA " FMT " CCC " FMT " CCG " FMT " CCT\n", dn[0x05], dn[0x05] / ndn, tn[0x14], tn[0x14] / ntn, tn[0x15], tn[0x15] / ntn, tn[0x17], tn[0x17] / ntn, tn[0x16], tn[0x16] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	668 fprintf(stdout, " " "%s" " " FMT " CG" FMT " CGA " FMT " CGC " FMT " CGG " FMT " CGT\n", gcat, dn[0x07], dn[0x07] / ndn, tn[0x1c], tn[0x1c] / ntn, tn[0x1d], tn[0x1d] / ntn, tn[0x1f], tn[0x1f] / ntn, tn[0x1e], tn[0x1e] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	669 fprintf(stdout, " " FMT " CT" FMT " CTA " FMT " CTC " FMT " CTG " FMT " CTT\n", dn[0x06], dn[0x06] / ndn, tn[0x18], tn[0x18] / ntn, tn[0x19], tn[0x19] / ntn, tn[0x1b], tn[0x1b] / ntn, tn[0x1a], tn[0x1a] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	670 fprintf(stdout, " " FMT " GA" FMT " GAA " FMT " GAC " FMT " GAG " FMT " GAT\n", dn[0x0c], dn[0x0c] / ndn, tn[0x30], tn[0x30] / ntn, tn[0x31], tn[0x31] / ntn, tn[0x33], tn[0x33] / ntn, tn[0x32], tn[0x32] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	671 fprintf(stdout, " " FMT " GC" FMT " GCA " FMT " GCC " FMT " GCG " FMT " GCT\n", dn[0x0d], dn[0x0d] / ndn, tn[0x34], tn[0x34] / ntn, tn[0x35], tn[0x35] / ntn, tn[0x37], tn[0x37] / ntn, tn[0x36], tn[0x36] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	672 fprintf(stdout, " " FMT " GG" FMT " GGA " FMT " GGC " FMT " GGG " FMT " GGT\n", dn[0x0f], dn[0x0f] / ndn, tn[0x3c], tn[0x3c] / ntn, tn[0x3d], tn[0x3d] / ntn, tn[0x3f], tn[0x3f] / ntn, tn[0x3e], tn[0x3e] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	673 fprintf(stdout, " " FMT " GT" FMT " GTA " FMT " GTC " FMT " GTG " FMT " GTT\n", dn[0x0e], dn[0x0e] / ndn, tn[0x38], tn[0x38] / ntn, tn[0x39], tn[0x39] / ntn, tn[0x3b], tn[0x3b] / ntn, tn[0x3a], tn[0x3a] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	674 fprintf(stdout, " " FMT " TA" FMT " TAA " FMT " TAC " FMT " TAG " FMT " TAT\n", dn[0x08], dn[0x08] / ndn, tn[0x20], tn[0x20] / ntn, tn[0x21], tn[0x21] / ntn, tn[0x23], tn[0x23] / ntn, tn[0x22], tn[0x22] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	675 fprintf(stdout, " " FMT " TC" FMT " TCA " FMT " TCC " FMT " TCG " FMT " TCT\n", dn[0x09], dn[0x09] / ndn, tn[0x24], tn[0x24] / ntn, tn[0x25], tn[0x25] / ntn, tn[0x27], tn[0x27] / ntn, tn[0x26], tn[0x26] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	676 fprintf(stdout, " " FMT " TG" FMT " TGA " FMT " TGC " FMT " TGG " FMT " TGT\n", dn[0x0b], dn[0x0b] / ndn, tn[0x2c], tn[0x2c] / ntn, tn[0x2d], tn[0x2d] / ntn, tn[0x2f], tn[0x2f] / ntn, tn[0x2e], tn[0x2e] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	677 fprintf(stdout, " " FMT " TT" FMT " TTA " FMT " TTC " FMT " TTG " FMT " TTT\n", dn[0x0a], dn[0x0a] / ndn, tn[0x28], tn[0x28] / ntn, tn[0x29], tn[0x29] / ntn, tn[0x2b], tn[0x2b] / ntn, tn[0x2a], tn[0x2a] / ntn);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	678 fprintf(stdout, "\n");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	679 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	680
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	681 delete [] shortLengths;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	682 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty fubar parents: diff changeset	683

Mercurial > repos > fubar > microsatbed

annotate seqrequester/src/seqrequester/summarize.C @ 1:1085e094cf5f draft