Merge pull request #307 from PolinaBevad/changes_for_option_M

Added fixes to integration tests

Author: pcingola

tests/integration/expected/vardict.paired.vcf

@@ -14,6 +14,8 @@
 ##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
 ##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
 ##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">
+##INFO=<ID=P0.01Likely,Number=0,Type=Flag,Description="Likely candidate but p-value > 0.01/5**vd2 (means the evidence in tumor sample might be weak, e.g. small diff in AF)">
+##INFO=<ID=IndelLikely,Number=0,Type=Flag,Description="Likely indels more than 2bp are not considered somatic (weak evidence of presence in normal samples)">
 ##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
 ##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">
 ##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
@@ -26,8 +28,6 @@
 ##FILTER=<ID=f0.02,Description="Allele frequency < 0.02">
 ##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05">
 ##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">
-##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">
-##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">
 ##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">
 ##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
 ##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">

tests/integration/tests_integration.sh

@@ -217,6 +217,11 @@ function run_perl_java {
     cat $VARDICT_OUT_R_JAVA | $VARDICTPERL_VAR_PAIRED > $VARDICT_OUT_VCF_JAVA
     cat $VARDICT_OUT_R_PERL | $VARDICTPERL_VAR_PAIRED > $VARDICT_OUT_VCF_PERL
     diff_results "VCF_JAVA_PERL" $VARDICT_OUT_VCF_PERL $VARDICT_OUT_VCF_JAVA
+
+    echo Running Var2VCF script opt_M
+    cat $VARDICT_OUT_R_JAVA | $VARDICTPERL_VAR_PAIRED -M > $VARDICT_OUT_VCF_JAVA
+    cat $VARDICT_OUT_R_PERL | $VARDICTPERL_VAR_PAIRED -M > $VARDICT_OUT_VCF_PERL
+    diff_results "VCF_JAVA_PERL_M" $VARDICT_OUT_VCF_PERL $VARDICT_OUT_VCF_JAVA
 }
 
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