# HG changeset patch # User lparsons # Date 1457986847 14400 # Node ID 13cad5d36301cb2672c87d1a087e73e4f134da36 # Parent c92ea5a8dec6376fa117374d51c163fc47e6403f planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty diff -r c92ea5a8dec6 -r 13cad5d36301 tool-dependencies/trtrR-1.0.0/Makefile --- a/tool-dependencies/trtrR-1.0.0/Makefile Mon Mar 14 16:18:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -trtr : trtr.c - cc trtr.c -o trtr - -clean : - rm trtr - - - - - diff -r c92ea5a8dec6 -r 13cad5d36301 tool-dependencies/trtrR-1.0.0/trtr Binary file tool-dependencies/trtrR-1.0.0/trtr has changed diff -r c92ea5a8dec6 -r 13cad5d36301 tool-dependencies/trtrR-1.0.0/trtr.c --- a/tool-dependencies/trtrR-1.0.0/trtr.c Mon Mar 14 16:18:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,221 +0,0 @@ -/********************************************************************** -* Author: Jonathan Richards -* Date: 12/11/2014 -* -* This tool removes tandem repeats from ends of unaligned sequencing -* reads (leaving one copy). This prevents reads that don't span the -* repeated region from overlapping and leading to innaccurate SNPs -* calls. -* -* The maximimum repeat length is adjustable (use 1 to trim only -* homopolymers). -* -* The "aggressive" option should not be touched in general. Setting to -* 0 will prevent the program from trimming to exactly 1 copy of the -* repeat, instead leaving between 1 and 2 copies. Why this would be -* useful, I don't know. -* -* This program could also be a useful first step before assembly. More -* testing needs to be done. -* -* Special thanks to my advisor, Professor Alison Gammie, for bringing -* this problem to my attention and to my reseach partner, Mitchell -* Vollger, for help testing and finalizing. -**********************************************************************/ - -#include -#include -#include -#include -#include -#include - -//use my getline for portability -//adapted from getline.c written by Jan Brittenson, bson@gnu.ai.mit.edu -//http://www.opensource.apple.com/source/cvs/cvs-19/cvs/lib/getline.c -ssize_t getline(char** lineptr, size_t* n, FILE* stream) { - size_t nchars_avail; - char* read_pos; - int save_errno; - ssize_t ret; - register int c; - - if (!lineptr || !n || !stream) { - errno = EINVAL; - return -1; - } - if (!*lineptr) { - *n = 128; - *lineptr = malloc(*n); - if (!*lineptr) { - errno = ENOMEM; - return -1; - } - } - nchars_avail = *n; - read_pos = *lineptr; - for (;;) { - c = getc(stream); - save_errno = errno; - if (c != '\r') { //for portability... - assert((*lineptr+*n)==(read_pos+nchars_avail)); - if (nchars_avail < 2) { - *n *= 2; - nchars_avail = *n + *lineptr - read_pos; - *lineptr = realloc(*lineptr, *n); - if (!*lineptr) { - errno = ENOMEM; - return -1; - } - read_pos = *n - nchars_avail + *lineptr; - assert((*lineptr+*n) == (read_pos+nchars_avail)); - } - if (ferror(stream)) { - errno = save_errno; - return -1; - } - if (c == EOF) { - if (read_pos == *lineptr) - return -1; - else - break; - } - *read_pos++ = c; - nchars_avail--; - if (c == '\n') - break; - } - } - *read_pos = '\0'; - ret = read_pos - *lineptr; - return ret; -} - -int main(int argc, char *argv[]) { - char *line = NULL; - size_t len = 0; - ssize_t line_length; - - int count = 0; - size_t leftTrim = 0; - size_t rightTrim = 0; - size_t i; - size_t i_max = 10; - size_t j; - size_t r; - size_t length; - size_t longest_region; - char *ptr; - bool matched = false; - bool aggressive_trim = true; - - FILE *file = fopen(argv[1], "r"); - - if (argc >= 3) { - i_max = strtol(argv[2], &ptr, 10); - if (argc >= 4) { - aggressive_trim = strtol(argv[3], &ptr, 10); - } - } - if (file != NULL) { - while ((line_length = getline(&line, &len, file)) != -1) { - count++; - switch (count) { - - //read name - case 1: - fputs(line, stdout); - break; - - //read sequence - case 2: - //find leftTrim - longest_region = 0; - for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat - if (line[0] == line[i]) { - matched = true; - j=1; - r=0; - while (matched == true) { - if (j == i) { - r++; - j=0; - } else if (line[j] != line[(r+1)*i+j]) { - //no length comparison needed because of \n at end - matched = false; - if (aggressive_trim) { - length = r*i+j; - } else { - length = r*i; - } - if (length > longest_region && r>0) { - longest_region = length; - } - } else { - j++; - } - } - - } - } - leftTrim = longest_region; - - //find rightTrim - longest_region = 0; - for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat - if (line[line_length-2] == line[line_length-2-i]) { - matched = true; - j=1; - r=0; - while (matched == true) { - if (j == i) { - r++; - j=0; - } else if ((line[line_length-2-j] != line[line_length-2-(r+1)*i-j]) - || line_length-2-(r+1)*i-j == leftTrim) { - matched = false; - if (aggressive_trim) { - length = r*i+j; - } else { - length = r*i; - } - if (length > longest_region && r>0) { - longest_region = length; - } - } else { - j++; - } - } - } - } - rightTrim = line_length-longest_region-1; - - //print trimmed line - line[rightTrim] = '\n'; - line[rightTrim+1] = '\0'; - fputs(line+leftTrim, stdout); - break; - - //+ - case 3: - fputs(line, stdout); - break; - - //read qualities - case 4: - count = 0; //reset to read title - line[rightTrim] = '\n'; - line[rightTrim+1] = '\0'; - fputs(line+leftTrim, stdout); - break; - default: - break; - } - } - free(line); - fclose(file); - } else { - perror(argv[1]); - } - return 0; -} \ No newline at end of file diff -r c92ea5a8dec6 -r 13cad5d36301 tool-dependencies/v1.0.0.tar.gz Binary file tool-dependencies/v1.0.0.tar.gz has changed