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1 #! /usr/bin/env perl
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2 #
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3 # Copyright (C) 2013 Genome Research Ltd.
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4 #
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5 # Author: James Bonfield <jkb@sanger.ac.uk>
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6 #
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7 # Permission is hereby granted, free of charge, to any person obtaining a copy
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8 # of this software and associated documentation files (the "Software"), to deal
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9 # in the Software without restriction, including without limitation the rights
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10 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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11 # copies of the Software, and to permit persons to whom the Software is
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12 # furnished to do so, subject to the following conditions:
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13 #
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14 # The above copyright notice and this permission notice shall be included in
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15 # all copies or substantial portions of the Software.
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16 #
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17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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20 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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22 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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23 # DEALINGS IN THE SOFTWARE.
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24 use strict;
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25 use warnings;
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26
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27 my $err_count = 0;
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28 my $suc_count = 0;
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29
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30 sub test {
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31 my ($cmd) = @_;
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32 print " $cmd\n";
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33 if (system("$cmd || exit 1") != 0) {
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34 print "FAIL $!\n";
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35 $err_count++;
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36 } else {
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37 $suc_count++;
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38 }
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39 }
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40
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41 foreach my $sam (glob("*#*.sam")) {
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42 my ($base, $ref) = ($sam =~ /((.*)#.*)\.sam/);
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43 $ref .= ".fa";
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44
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45 my $bam = "$base.tmp.bam";
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46 my $cram = "$base.tmp.cram";
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47
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48 print "\n=== Testing $sam, ref $ref ===\n";
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49
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50 # SAM -> BAM -> SAM
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51 test "./test_view -S -b $sam > $bam";
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52 test "./test_view $bam > $bam.sam_";
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53 test "./compare_sam.pl $sam $bam.sam_";
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54
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55 # SAM -> CRAM -> SAM
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56 test "./test_view -t $ref -S -C $sam > $cram";
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57 test "./test_view -D $cram > $cram.sam_";
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58 test "./compare_sam.pl -nomd $sam $cram.sam_";
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59
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60 # BAM -> CRAM -> BAM -> SAM
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61 $cram = "$bam.cram";
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62 test "./test_view -t $ref -C $bam > $cram";
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63 test "./test_view -b -D $cram > $cram.bam";
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64 test "./test_view $cram.bam > $cram.bam.sam_";
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65 test "./compare_sam.pl -nomd $sam $cram.bam.sam_";
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66 }
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67
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68 print "\nSuccesses $suc_count\n";
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69 print "\nFailures $err_count\n";
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70
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71 exit ($err_count > 0);
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