ex-231 (cgates): Adjusted so merge logs once per command; minor cleanup

umich-brcf-bioinf · Apr 22, 2015 · 3a97fa2 · 3a97fa2
1 parent d5296ff
commit 3a97fa2
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Showing 5 changed files with 7 additions and 6 deletions.
diff --git a/jacquard/merge.py b/jacquard/merge.py
@@ -45,9 +45,10 @@
 _DEFAULT_INCLUDED_FORMAT_TAGS = ["JQ_.*"]
 _MULT_ALT_TAG = "JQ_MULT_ALT_LOCUS"
 _JQ_SOMATIC_TAG = "HC_SOM"
-#TODO: (jebene) is the description of this really accurate?
+
 _MULT_ALT_HEADER = ('##INFO=<ID={},Number=0,Type=Flag,'
-                    'Description="dbSNP Membership">').format(_MULT_ALT_TAG)
+                    'Description="More than one alt allele was seen at this '
+                    'locus.">').format(_MULT_ALT_TAG)
 _FILE_FORMAT = ["##fileformat=VCFv4.1"]
 _FILE_OUTPUT_SUFFIX = "merged"
 

diff --git a/test/functional_tests/02_merge/benchmark/merged.vcf b/test/functional_tests/02_merge/benchmark/merged.vcf
@@ -6,7 +6,7 @@
 ##contig=<ID=chr2,length=243199373>
 ##contig=<ID=chr3,length=198022430>
 ##contig=<ID=chr13,length=115169878>
-##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">
 ##FORMAT=<ID=JQ_MT_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 2 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Float,Description="Jacquard depth for MuTect (based on DP)">
 ##FORMAT=<ID=JQ_MT_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for MuTect: 0=non-somatic,1=somatic (based on SS FORMAT tag)">

diff --git a/test/functional_tests/jacquard_test/merge/benchmark/merged.vcf b/test/functional_tests/jacquard_test/merge/benchmark/merged.vcf
@@ -3,7 +3,7 @@
 ##jacquard.merge.sample=<Column=2,Name=tiny|TUMOR,Source=tiny.mutect.translatedTags.vcf|tiny.strelka.indels.translatedTags.vcf|tiny.strelka.snvs.translatedTags.vcf|tiny.varscan.indel.translatedTags.vcf|tiny.varscan.snp.translatedTags.vcf>
 ##jacquard=<Timestamp="2015-04-20 11:48:47",Command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",Cwd="C:\Users\jebene\git">
 ##contig=<ID=chr1,length=249250621>
-##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">
 ##FORMAT=<ID=JQ_MT_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 2 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
 ##FORMAT=<ID=JQ_MT_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">

diff --git a/test/functional_tests/jacquard_test/summarize/benchmark/summarized.vcf b/test/functional_tests/jacquard_test/summarize/benchmark/summarized.vcf
@@ -8,7 +8,7 @@
 ##jacquard=<Timestamp="2015-04-20 11:48:47",Command="<module 'jacquard.merge' from 'C:\Users\jebene\git\Jacquard\jacquard\merge.pyc'>",Cwd="C:\Users\jebene\git">
 ##jacquard=<Timestamp="2015-04-20 11:51:19",Command="<module 'jacquard.summarize' from 'C:\Users\jebene\git\Jacquard\jacquard\summarize.pyc'>",Cwd="C:\Users\jebene\git">
 ##contig=<ID=chr1,length=249250621>
-##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">
 ##INFO=<ID=JQ_SUMMARY_SAMPLES_PASSED_COUNT,Number=1,Type=Integer,Description="Count of samples where a variant caller passed the filter in any of the Jacquard tagged VCFs">
 ##INFO=<ID=JQ_SUMMARY_SAMPLES_REPORTED_COUNT,Number=1,Type=Integer,Description="Count of samples where this variant appeared in any of the Jacquard tagged VCFs (regardless of quality/filtering)">
 ##FORMAT=<ID=JQ_MT_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 2 digits (based on FA)">

diff --git a/test/merge_test.py b/test/merge_test.py
@@ -987,7 +987,7 @@ def test_execute_includeFormatIds(self):
                                    "##jacquard.merge.sample=<Column=2,Name=P1|SampleB,Source=P1.fileA.vcf>\n",
                                    '##contig=<ID=chr1,Number=1>\n',
                                    '##contig=<ID=chr2,Number=1>\n',
-                                   '##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="dbSNP Membership">\n',
+                                   '##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">\n',
                                    '##FORMAT=<ID=Bar,Number=1,Type=Float,Description="bar">\n',
                                    '##FORMAT=<ID=JQ_Foo,Number=1,Type=Float,Description="foo">\n',
                                    "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tP1|SampleA\tP1|SampleB\n"]