changeset 31:13cad5d36301

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty

--- 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
-
-
-
-
-

Binary file tool-dependencies/trtrR-1.0.0/trtr has changed

--- 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 <stdio.h>
-#include <stdlib.h>
-#include <stdbool.h>
-#include <sys/types.h>
-#include <assert.h>
-#include <errno.h>
-
-//use my getline for portability
-//adapted from getline.c written by Jan Brittenson, [e-mail]
-//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

Binary file tool-dependencies/v1.0.0.tar.gz has changed