Resolve conflict in c/c_tests/test_04_mismatchQc.sh

CHANGES.md

@@ -1,5 +1,10 @@
 # CHANGES
 
+## 4.2.6
+
+* New bam file added with mini reference for cram formatting test.
+* This prevents travis timeout issues where the reference area is being searched for by bamvalidate
+
 ## 4.2.5
 
 * mismatchQC has added commandline parameter - used by default

c/c_tests/test_04_mismatchQc.sh

@@ -46,39 +46,34 @@ compare_sam () {
 }
 
 #Ensure valid format produced
-echo "1"
 ../bin/mismatchQc -i ../t/data/mismatch_test.bam | bamvalidate
 if [ "$?" != "0" ];
 then
   echo "ERROR running ../bin/mismatchQc -i ../t/data/mismatch_test.bam. Invalid output"
   exit 1;
 fi
 
-echo "2"
 ../bin/mismatchQc -i ../t/data/mismatch_test.bam -l 2| bamvalidate
 if [ "$?" != "0" ];
 then
   echo "ERROR running ../bin/mismatchQc -i ../t/data/mismatch_test.bam -l 2. Invalid output with compression levels"
   exit 1;
 fi
 
-echo "3"
-../bin/mismatchQc -i ../t/data/mismatch_test.bam -C | bamvalidate inputformat=cram
+../bin/mismatchQc -i ../t/data/mismatch_test.cram -C | bamvalidate inputformat=cram
 if [ "$?" != "0" ];
 then
   echo "ERROR running ../bin/mismatchQc -i ../t/data/mismatch_test.bam -C. Invalid output cram compression"
   exit 1;
 fi
 
-echo "4"
 ../bin/mismatchQc -i ../t/data/mismatch_test.bam | bamcollate2 inputformat=bam outputformat=sam collate=0 resetaux=0 > ../t/data/mismatch_test_out.sam;
 if [ "$?" != "0" ];
 then
   echo "ERROR running ../bin/mismatchQc -i ../t/data/mismatch_test.bam | samtools view -h -o ../t/data/mismatch_test_out.sam"
   exit 1;
 fi
 
-echo "5"
 if [ compare_sam '../t/data/mismatch_test_out.sam' '../t/data/mismatch_expected_out.sam' != "0" ];
 then
   echo "ERROR in "$0": Comparing mismatchQc to expected result failed."
@@ -87,15 +82,13 @@ then
   exit 1
 fi
 
-echo "6"
 ../bin/mismatchQc -i ../t/data/mismatch_test.bam -t 0.01 | bamcollate2 inputformat=bam outputformat=sam collate=0 resetaux=0 > ../t/data/mismatch_test_out.sam;
 if [ "$?" != "0" ];
 then
   echo "ERROR running ../bin/mismatchQc -i ../t/data/mismatch_test.bam | samtools view -h -o ../t/data/mismatch_test_out.sam"
   exit 1;
 fi
 
-echo "7"
 if [ compare_sam '../t/data/mismatch_test_out.sam' '../t/data/mismatch_expected_out_low_frac.sam' != "0" ];
 then
   echo "ERROR in "$0": Comparing mismatchQc low fraction to expected result failed."

lib/PCAP.pm

@@ -27,7 +27,7 @@ use FindBin qw($Bin);
 use File::Which qw(which);
 # don't use autodie, only core perl in here
 
-our $VERSION = '4.2.5';
+our $VERSION = '4.2.6';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

t/data/test.fa.fai

@@ -0,0 +1 @@
+22	51304566	4	60	61