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view fastx_toolkit-0.0.6/src/fastx_trimmer/fastx_trimmer.c @ 3:997f5136985f draft default tip
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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009 A. Gordon (gordon@cshl.edu) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. */ #include <limits.h> #include <stdio.h> #include <stdlib.h> #include <string.h> #include <getopt.h> #include <errno.h> #include <err.h> #include <config.h> #include "fastx.h" #include "fastx_args.h" #define MAX_ADAPTER_LEN 100 const char* usage= "usage: fastx_trimmer [-h] [-f N] [-l N] [-z] [-v] [-i INFILE] [-o OUTFILE]\n" \ "\n" \ "version " VERSION "\n" \ " [-h] = This helpful help screen.\n" \ " [-f N] = First base to keep. Default is 1 (=first base).\n" \ " [-l N] = Last base to keep. Default is entire read.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ "\n"; #define DO_NOT_TRIM_LAST_BASE (0) int keep_first_base=1; int keep_last_base=DO_NOT_TRIM_LAST_BASE; FASTX fastx; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'f': if (optarg==NULL) errx(1, "[-f] parameter requires an argument value"); keep_first_base = strtoul(optarg,NULL,10); if (keep_first_base<=0 || keep_first_base>=MAX_SEQ_LINE_LENGTH) errx(1,"Invalid number bases to keep (-f %s)", optarg); break; case 'l': if (optarg==NULL) errx(1, "[-l] parameter requires an argument value"); keep_last_base = strtoul(optarg,NULL,10); if (keep_last_base<=0 || keep_last_base>=MAX_SEQ_LINE_LENGTH) errx(1,"Invalid number bases to keep (-l %s)", optarg); break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { size_t i; fastx_parse_cmdline(argc, argv, "l:f:", parse_program_args); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { if (keep_last_base != DO_NOT_TRIM_LAST_BASE) { fastx.nucleotides[keep_last_base] = 0 ; } if (keep_first_base != 1) { for (i=0; i < strlen(fastx.nucleotides)-keep_first_base+1 ; i++) { fastx.nucleotides[i] = fastx.nucleotides[i+keep_first_base-1]; fastx.quality[i] = fastx.quality[i+keep_first_base-1]; } fastx.nucleotides[i] = 0 ; } //none of the above condition matched, so print this sequence. fastx_write_record(&fastx); } if ( verbose_flag() ) { fprintf(get_report_file(), "Trimming: base %d to %d\n", keep_first_base, keep_last_base ) ; fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; } return 0; }