fix bug introduced in v0.2.8

thanks very much to Steve for reporting and providing test-case.

Author: brentp

src/slivarpkg/gnotate.nim

@@ -101,6 +101,7 @@ proc parseLong(line: string, n_fields:int): Long {.inline.} =
 
 
 proc readLongs(g:var Gnotater, chrom: string) =
+  g.longs.setLen(0)
 
   var big = newString(16)
   doAssert g.zip.read_into(&"sli.var/{chrom}/long-alleles.txt", big)

src/slivarpkg/version.nim

@@ -1,2 +1,2 @@
-const slivarVersion* = "0.2.8"
+const slivarVersion* = "0.2.9"
 const slivarGitCommit* = staticExec("git rev-parse --verify HEAD")

tests/functional-tests.sh

@@ -54,6 +54,7 @@ assert_equal "0" "$(bcftools view -H -i 'FMT/DP[0] <= 10 || FMT/DP[1] <= 10 || F
 assert_equal 11 $(bcftools view -H xx.bcf | wc -l)
 
 
+
 run check_denovo_with_filter $exe expr --js js/slivar-functions.js -v tests/ashk-trio.vcf.gz --pass-only --trio "denovo:variant.FILTER == 'PASS' && kid.alts == 1 && mom.alts == 0 && dad.alts == 0 && (mom.AD[1] + dad.AD[1]) < 2 && kid.GQ > 10 && mom.GQ > 10 && dad.GQ > 10 && kid.DP > 10 && mom.DP > 10 && dad.DP > 10" --ped tests/ashk-trio.ped -o xx.bcf
 
 assert_exit_code 0
@@ -217,3 +218,10 @@ assert_in_stderr "[slivar] warning! BCSQ has a CSQ of @63280473 which is incompl
 [slivar] warning! BCSQ has a CSQ of @788407 which is incomplete. skipping chr16:793183(G/A)
 [slivar] warning! BCSQ has a CSQ of @3592545 which is incomplete. skipping chr19:3593228(G/A)"
 rm x.vcf.gz
+
+
+run check_indel_bug_setup $exe make-gnotate -f AF:gno_af tests/indel-bug.vcf --prefix tests/indel-bug
+run check_indel_bug $exe expr -g tests/indel-bug.zip -v tests/indel-bug.vcf -o x.vcf
+assert_equal 0 $(bcftools query -f "%AF\t%gno_af"  x.vcf | awk '$1 != $2' | wc -l)
+rm x.vcf
+

tests/indel-bug.vcf

@@ -0,0 +1,19 @@
+##fileformat=VCFv4.2							
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=AF,Number=1,Type=Float,Description="field from from gnotate VCF">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr3	57446013	.	ATAAATAAATAAT	A	230919	PASS	AF=0.574454
+chr4	443460	.	CCACATGTGTAGGGTTTCTCTCCAGTATGAATTCTCCTATGTACATAAAGGTTTGCGGACTGTCTAAAGGCTTTGCCACATACTT	C	274.8	PASS	AF=0
+chr5	80300545	.	G	GTCCCTCTCCCTC	114541	PASS	AF=0.386214
+chr6	31028873	.	A	ACCTCTACTGAAGGCTCTGAGACCACCACAG	13662.3	PASS	AF=0.1145
+chr6	31028943	.	C	CAGGCTCTGAGACCACCACAGCCTCTACTGA	7768.74	PASS	AF=0.048706
+chr9	32986034	.	AAAAAAAAACAAAAAAAAAAAC	A	118886	PASS	AF=0.476683
+chr9	35183034	.	CGCTCCTCACTTCCCAGATGGGGCGGCCGGGCAGAGGCGCTCCTCACCTCCCAGACGGGGCGGCCTGGCAGAGGT	C	56269	PASS	AF=0.229961
+chr10	2501862	.	ACCCGGCTCACCTCAACAACAAAGCGCGGTTTCCTCCCTCGCCATCCTTCCTCG	A	99790.2	PASS	AF=0.186495
+chr10	42429112	.	TCACCTTTGCTTGATATGATAATATAGTGCCAAGG	T	120274	PASS	AF=0.482119
+chr11	10353386	.	TTTTTCTTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC	T	11465.2	PASS	AF=0.652204
+chr16	3197578	.	TGGCCACATGTCAAGGGCTCCAGAGCCACCTGCTGCTGGGGGCCAGTTCCTCAGACAGCGCAGTCCTACATCTGACTACAAGCTTAAATG	T	212370	PASS	AF=0.67148
+chr17	40819040	.	AGCCGCCGCCGGAACTGCCGCCGTGGCCGCCGCCGTG	A	651.56	PASS	AF=0.00191424
+chr17	40819055	.	TGCCGCCGTGGCC	T	78807.4	PASS	AF=0.329802
+chr19	58404775	.	GGGCAGAGGGGCTCCTCATTTCCCAGTAGGGGCGGCCGGGCAGAGGCGCCCCTCACCTCCCGGACAGGGCGGCTCGCCAGGCGGGGGGCTGACCCCCCCCCCCACCTCCCTCCTGGACGGGGCGGCTGGCCA	G	1168.4	PASS	AF=0.0145961
+chr20	37179387	.	G	GCTTACAGACAGGGCCCCGCGGCCGGCACT	700721	PASS	AF=0.504156