Mercurial > repos > mrvollger > trtr

annotate tool-dependencies/trtrR-1.0.0/trtr.c @ 30:c92ea5a8dec6

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
author lparsons
date Mon, 14 Mar 2016 16:18:55 -0400
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30
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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1 /**********************************************************************
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2 * Author: Jonathan Richards
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3 * Date: 12/11/2014
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4 *
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5 * This tool removes tandem repeats from ends of unaligned sequencing
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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6 * reads (leaving one copy). This prevents reads that don't span the
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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7 * repeated region from overlapping and leading to innaccurate SNPs
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8 * calls.
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9 *
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10 * The maximimum repeat length is adjustable (use 1 to trim only
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11 * homopolymers).
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12 *
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13 * The "aggressive" option should not be touched in general. Setting to
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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14 * 0 will prevent the program from trimming to exactly 1 copy of the
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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15 * repeat, instead leaving between 1 and 2 copies. Why this would be
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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16 * useful, I don't know.
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17 *
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18 * This program could also be a useful first step before assembly. More
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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19 * testing needs to be done.
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20 *
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21 * Special thanks to my advisor, Professor Alison Gammie, for bringing
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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22 * this problem to my attention and to my reseach partner, Mitchell
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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23 * Vollger, for help testing and finalizing.
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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24 **********************************************************************/
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25
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26 #include <stdio.h>
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27 #include <stdlib.h>
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28 #include <stdbool.h>
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29 #include <sys/types.h>
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30 #include <assert.h>
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31 #include <errno.h>
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32
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33 //use my getline for portability
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34 //adapted from getline.c written by Jan Brittenson, bson@gnu.ai.mit.edu
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35 //http://www.opensource.apple.com/source/cvs/cvs-19/cvs/lib/getline.c
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36 ssize_t getline(char** lineptr, size_t* n, FILE* stream) {
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37 size_t nchars_avail;
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38 char* read_pos;
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39 int save_errno;
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40 ssize_t ret;
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41 register int c;
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42
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43 if (!lineptr || !n || !stream) {
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44 errno = EINVAL;
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45 return -1;
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46 }
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47 if (!*lineptr) {
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48 *n = 128;
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49 *lineptr = malloc(*n);
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50 if (!*lineptr) {
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51 errno = ENOMEM;
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52 return -1;
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53 }
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54 }
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55 nchars_avail = *n;
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56 read_pos = *lineptr;
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57 for (;;) {
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58 c = getc(stream);
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59 save_errno = errno;
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60 if (c != '\r') { //for portability...
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61 assert((*lineptr+*n)==(read_pos+nchars_avail));
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62 if (nchars_avail < 2) {
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63 *n *= 2;
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64 nchars_avail = *n + *lineptr - read_pos;
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65 *lineptr = realloc(*lineptr, *n);
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66 if (!*lineptr) {
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67 errno = ENOMEM;
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68 return -1;
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69 }
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70 read_pos = *n - nchars_avail + *lineptr;
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71 assert((*lineptr+*n) == (read_pos+nchars_avail));
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72 }
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73 if (ferror(stream)) {
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74 errno = save_errno;
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75 return -1;
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76 }
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77 if (c == EOF) {
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78 if (read_pos == *lineptr)
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79 return -1;
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80 else
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81 break;
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82 }
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83 *read_pos++ = c;
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84 nchars_avail--;
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85 if (c == '\n')
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86 break;
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87 }
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88 }
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89 *read_pos = '\0';
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
90 ret = read_pos - *lineptr;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
91 return ret;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
92 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
93
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
94 int main(int argc, char *argv[]) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
95 char *line = NULL;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
96 size_t len = 0;
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lparsons
parents:
diff changeset
97 ssize_t line_length;
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lparsons
parents:
diff changeset
98
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lparsons
parents:
diff changeset
99 int count = 0;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
100 size_t leftTrim = 0;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
101 size_t rightTrim = 0;
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lparsons
parents:
diff changeset
102 size_t i;
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lparsons
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103 size_t i_max = 10;
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lparsons
parents:
diff changeset
104 size_t j;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
105 size_t r;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
106 size_t length;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
107 size_t longest_region;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
108 char *ptr;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
109 bool matched = false;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
110 bool aggressive_trim = true;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
111
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
112 FILE *file = fopen(argv[1], "r");
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
113
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
114 if (argc >= 3) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
115 i_max = strtol(argv[2], &ptr, 10);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
116 if (argc >= 4) {
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lparsons
parents:
diff changeset
117 aggressive_trim = strtol(argv[3], &ptr, 10);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
118 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
119 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
120 if (file != NULL) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
121 while ((line_length = getline(&line, &len, file)) != -1) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
122 count++;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
123 switch (count) {
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lparsons
parents:
diff changeset
124
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lparsons
parents:
diff changeset
125 //read name
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
126 case 1:
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
127 fputs(line, stdout);
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lparsons
parents:
diff changeset
128 break;
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lparsons
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diff changeset
129
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lparsons
parents:
diff changeset
130 //read sequence
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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diff changeset
131 case 2:
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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132 //find leftTrim
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lparsons
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diff changeset
133 longest_region = 0;
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lparsons
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diff changeset
134 for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
135 if (line[0] == line[i]) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
136 matched = true;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
137 j=1;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
138 r=0;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
139 while (matched == true) {
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lparsons
parents:
diff changeset
140 if (j == i) {
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lparsons
parents:
diff changeset
141 r++;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
142 j=0;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
143 } else if (line[j] != line[(r+1)*i+j]) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
144 //no length comparison needed because of \n at end
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
145 matched = false;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
146 if (aggressive_trim) {
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lparsons
parents:
diff changeset
147 length = r*i+j;
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lparsons
parents:
diff changeset
148 } else {
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lparsons
parents:
diff changeset
149 length = r*i;
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lparsons
parents:
diff changeset
150 }
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lparsons
parents:
diff changeset
151 if (length > longest_region && r>0) {
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lparsons
parents:
diff changeset
152 longest_region = length;
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lparsons
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diff changeset
153 }
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lparsons
parents:
diff changeset
154 } else {
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lparsons
parents:
diff changeset
155 j++;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
156 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
157 }
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lparsons
parents:
diff changeset
158
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lparsons
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diff changeset
159 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
160 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
161 leftTrim = longest_region;
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lparsons
parents:
diff changeset
162
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lparsons
parents:
diff changeset
163 //find rightTrim
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
164 longest_region = 0;
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lparsons
parents:
diff changeset
165 for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
166 if (line[line_length-2] == line[line_length-2-i]) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
167 matched = true;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
168 j=1;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
169 r=0;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
170 while (matched == true) {
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lparsons
parents:
diff changeset
171 if (j == i) {
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lparsons
parents:
diff changeset
172 r++;
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lparsons
parents:
diff changeset
173 j=0;
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lparsons
parents:
diff changeset
174 } else if ((line[line_length-2-j] != line[line_length-2-(r+1)*i-j])
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lparsons
parents:
diff changeset
175 || line_length-2-(r+1)*i-j == leftTrim) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
176 matched = false;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
177 if (aggressive_trim) {
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lparsons
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diff changeset
178 length = r*i+j;
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lparsons
parents:
diff changeset
179 } else {
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lparsons
parents:
diff changeset
180 length = r*i;
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lparsons
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diff changeset
181 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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182 if (length > longest_region && r>0) {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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183 longest_region = length;
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lparsons
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184 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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185 } else {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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186 j++;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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187 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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188 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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189 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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190 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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191 rightTrim = line_length-longest_region-1;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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192
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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193 //print trimmed line
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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194 line[rightTrim] = '\n';
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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195 line[rightTrim+1] = '\0';
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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196 fputs(line+leftTrim, stdout);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
197 break;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
198
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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199 //+
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
200 case 3:
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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201 fputs(line, stdout);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
202 break;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
203
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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204 //read qualities
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
205 case 4:
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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206 count = 0; //reset to read title
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lparsons
parents:
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207 line[rightTrim] = '\n';
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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208 line[rightTrim+1] = '\0';
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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209 fputs(line+leftTrim, stdout);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
210 break;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
211 default:
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
212 break;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
213 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
214 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
215 free(line);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
216 fclose(file);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
217 } else {
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
218 perror(argv[1]);
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
219 }
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
diff changeset
220 return 0;
c92ea5a8dec6 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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221 }