ekg/vcflib — Issue #6: VariantCallFile.header includes extra "\n"
Author: arq5x
Created: 2012-03-05 12:44:17+00:00
State: open

Hi Erik,

It looks like an extra newline is being added to the header attribute when parsing the VCF file header. This is best illustrated by the vcfecho tool. Note the extra newline after the field definition.

$ ./vcfecho sample.vcf
##fileformat=VCFv4.0
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FILTER=
##FILTER=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##ALT=
##ALT=
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003

19	111	.	A	C	9.6	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
19	112	.	A	G	10	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
20	14370	rs6054257	G	A	29	PASS	AF=0.5;DP=14;NS=3;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
20	17330	.	T	A	3	q10	AF=0.017;DP=11;NS=3	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.,.
20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.,.
20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3	GT:GQ:DP:HQ	0|0:54:.:56,60	0|0:48:4:51,51	0/0:61:2:.,.
20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
20	1235237	.	T	.	50	.	GT	0/0	0|0	.
X	10	rsTest	AC	A,ATG	10	PASS	GT	0	0/1	0|2