added patternfile tester to patterngenerator

parklab · Mar 7, 2018 · d45a4fd · d45a4fd
1 parent 7f4abb8
commit d45a4fd
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Showing 3 changed files with 18 additions and 0 deletions.
diff --git a/ngscheckmate_fastq-source/patternconvert.h.gch b/ngscheckmate_fastq-source/patternconvert.h.gch
diff --git a/patterngenerator/makesnvpattern.pl b/patterngenerator/makesnvpattern.pl
@@ -12,3 +12,18 @@
 system("${scriptdir}filter_patters_based_on_ntm.pl $outdir/$outprefix.txt $outdir/$outprefix.ntm > $outdir/$outprefix.uniq.txt");
 system("${scriptdir}patternconverter $outdir/$outprefix.uniq.txt $outdir/$outprefix.pt");
 
+# test
+print("Checking pattern file...\n");
+system("${scriptdir}patterntestreader $outdir/$outprefix.pt $outdir/$outprefix.pt-txt");
+system("sort $outdir/$outprefix.pt-txt > $outdir/$outprefix.pt-txt.sorted");
+system("sort $outdir/$outprefix.uniq.txt > $outdir/$outprefix.uniq.txt.sorted");
+$diff=`diff $outdir/$outprefix.pt-txt.sorted $outdir/$outprefix.uniq.txt.sorted`;
+if($diff!~/\S/){
+  print("pattern file looks good!\n");
+  exit(0); 
+}
+else {
+  print("pattern file does not look good.\n");
+  exit(1);
+}
+
diff --git a/tests/test.sh b/tests/test.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 # patterngenerator test
 ./patterngenerator/makesnvpattern.pl tests/SNP_GRCh37_hg19_woChr_21part.bed tests/GRCh37_21part.multi.fa tests/GRCh37_21part tests out
@@ -8,3 +9,5 @@
 
 # remove test pattern files
 rm tests/out*
+
+set +e