Mercurial > repos > mrvollger > trtr
annotate tool-dependencies/trtrR-1.0.0/trtr.c @ 30:c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
author | lparsons |
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date | Mon, 14 Mar 2016 16:18:55 -0400 |
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rev | line source |
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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 /********************************************************************** |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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2 * Author: Jonathan Richards |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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3 * Date: 12/11/2014 |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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4 * |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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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 |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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8 * calls. |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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9 * |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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10 * The maximimum repeat length is adjustable (use 1 to trim only |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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11 * homopolymers). |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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12 * |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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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. |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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17 * |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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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
lparsons
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19 * testing needs to be done. |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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20 * |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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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
lparsons
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24 **********************************************************************/ |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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25 |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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26 #include <stdio.h> |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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27 #include <stdlib.h> |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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28 #include <stdbool.h> |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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29 #include <sys/types.h> |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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30 #include <assert.h> |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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31 #include <errno.h> |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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32 |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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33 //use my getline for portability |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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34 //adapted from getline.c written by Jan Brittenson, bson@gnu.ai.mit.edu |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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35 //http://www.opensource.apple.com/source/cvs/cvs-19/cvs/lib/getline.c |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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36 ssize_t getline(char** lineptr, size_t* n, FILE* stream) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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37 size_t nchars_avail; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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38 char* read_pos; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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39 int save_errno; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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40 ssize_t ret; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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41 register int c; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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42 |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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43 if (!lineptr || !n || !stream) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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44 errno = EINVAL; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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45 return -1; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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46 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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47 if (!*lineptr) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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48 *n = 128; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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49 *lineptr = malloc(*n); |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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50 if (!*lineptr) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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51 errno = ENOMEM; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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52 return -1; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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53 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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54 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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55 nchars_avail = *n; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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56 read_pos = *lineptr; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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57 for (;;) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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58 c = getc(stream); |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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59 save_errno = errno; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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60 if (c != '\r') { //for portability... |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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61 assert((*lineptr+*n)==(read_pos+nchars_avail)); |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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62 if (nchars_avail < 2) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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63 *n *= 2; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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64 nchars_avail = *n + *lineptr - read_pos; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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65 *lineptr = realloc(*lineptr, *n); |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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66 if (!*lineptr) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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67 errno = ENOMEM; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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68 return -1; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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69 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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70 read_pos = *n - nchars_avail + *lineptr; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
parents:
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71 assert((*lineptr+*n) == (read_pos+nchars_avail)); |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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72 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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73 if (ferror(stream)) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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74 errno = save_errno; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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75 return -1; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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76 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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77 if (c == EOF) { |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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78 if (read_pos == *lineptr) |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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79 return -1; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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80 else |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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81 break; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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82 } |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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83 *read_pos++ = c; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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84 nchars_avail--; |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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85 if (c == '\n') |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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86 break; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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87 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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88 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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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
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90 ret = read_pos - *lineptr; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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91 return ret; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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92 } |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
lparsons
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93 |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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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
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95 char *line = NULL; |
c92ea5a8dec6
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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96 size_t len = 0; |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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97 ssize_t line_length; |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
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98 |
c92ea5a8dec6
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99 int count = 0; |
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100 size_t leftTrim = 0; |
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101 size_t rightTrim = 0; |
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102 size_t i; |
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103 size_t i_max = 10; |
c92ea5a8dec6
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104 size_t j; |
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105 size_t r; |
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106 size_t length; |
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107 size_t longest_region; |
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108 char *ptr; |
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109 bool matched = false; |
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110 bool aggressive_trim = true; |
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111 |
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112 FILE *file = fopen(argv[1], "r"); |
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113 |
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114 if (argc >= 3) { |
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115 i_max = strtol(argv[2], &ptr, 10); |
c92ea5a8dec6
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116 if (argc >= 4) { |
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117 aggressive_trim = strtol(argv[3], &ptr, 10); |
c92ea5a8dec6
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118 } |
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119 } |
c92ea5a8dec6
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120 if (file != NULL) { |
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121 while ((line_length = getline(&line, &len, file)) != -1) { |
c92ea5a8dec6
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122 count++; |
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123 switch (count) { |
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124 |
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125 //read name |
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126 case 1: |
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127 fputs(line, stdout); |
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128 break; |
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129 |
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130 //read sequence |
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131 case 2: |
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132 //find leftTrim |
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133 longest_region = 0; |
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134 for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat |
c92ea5a8dec6
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135 if (line[0] == line[i]) { |
c92ea5a8dec6
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136 matched = true; |
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137 j=1; |
c92ea5a8dec6
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138 r=0; |
c92ea5a8dec6
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139 while (matched == true) { |
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140 if (j == i) { |
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141 r++; |
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142 j=0; |
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143 } else if (line[j] != line[(r+1)*i+j]) { |
c92ea5a8dec6
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144 //no length comparison needed because of \n at end |
c92ea5a8dec6
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145 matched = false; |
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146 if (aggressive_trim) { |
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147 length = r*i+j; |
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148 } else { |
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149 length = r*i; |
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150 } |
c92ea5a8dec6
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151 if (length > longest_region && r>0) { |
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152 longest_region = length; |
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153 } |
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154 } else { |
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155 j++; |
c92ea5a8dec6
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156 } |
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157 } |
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158 |
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159 } |
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160 } |
c92ea5a8dec6
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161 leftTrim = longest_region; |
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162 |
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163 //find rightTrim |
c92ea5a8dec6
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164 longest_region = 0; |
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165 for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat |
c92ea5a8dec6
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166 if (line[line_length-2] == line[line_length-2-i]) { |
c92ea5a8dec6
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167 matched = true; |
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168 j=1; |
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169 r=0; |
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170 while (matched == true) { |
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171 if (j == i) { |
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172 r++; |
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173 j=0; |
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174 } else if ((line[line_length-2-j] != line[line_length-2-(r+1)*i-j]) |
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175 || line_length-2-(r+1)*i-j == leftTrim) { |
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176 matched = false; |
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177 if (aggressive_trim) { |
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178 length = r*i+j; |
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179 } else { |
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180 length = r*i; |
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181 } |
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182 if (length > longest_region && r>0) { |
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183 longest_region = length; |
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184 } |
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185 } else { |
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186 j++; |
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187 } |
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188 } |
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189 } |
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190 } |
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191 rightTrim = line_length-longest_region-1; |
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192 |
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193 //print trimmed line |
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194 line[rightTrim] = '\n'; |
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195 line[rightTrim+1] = '\0'; |
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196 fputs(line+leftTrim, stdout); |
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197 break; |
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198 |
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199 //+ |
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200 case 3: |
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201 fputs(line, stdout); |
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202 break; |
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203 |
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204 //read qualities |
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205 case 4: |
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206 count = 0; //reset to read title |
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207 line[rightTrim] = '\n'; |
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208 line[rightTrim+1] = '\0'; |
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209 fputs(line+leftTrim, stdout); |
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210 break; |
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211 default: |
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212 break; |
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213 } |
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214 } |
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215 free(line); |
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216 fclose(file); |
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217 } else { |
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218 perror(argv[1]); |
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219 } |
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220 return 0; |
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221 } |