11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/htslib/test/test-vcf-api.out src/htslib/test/test-vcf-api.out
new file mode 100644
index 0000000..d3bb73e
--- /dev/null
+++ src/htslib/test/test-vcf-api.out
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20090805
+##unused=<XX=AA,Description="Unused generic">
+##source=myImputationProgramV3.1
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=TS,Number=1,Type=String,Description="Test String">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ:TS	0|0:48:1:51,51:String1	1|0:48:8:51,51:SomeOtherString2	1/1:43:5:.,.:YetAnotherString3
+20	14370	.	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:DP:HQ:TS	0|0:1:51,51:String1	1|0:8:51,51:SomeOtherString2	1/1:5:.,.:YetAnotherString3
+20	14370	.	G	A	29	PASS	NS=3;DP=99;AF=0.5;DB;H2	GT:DP:HQ:TS	0|0:9:51,51:String1	1|0:9:51,51:SomeOtherString2	1/1:9:.,.:YetAnotherString3
+20	1110696	.	A	G,T	67	.	NS=2;DP=10;AF=0.333,.;AA=T;DB	GT	2	1	./.
+20	1110696	.	A	G,T	67	.	NS=2;DP=10;AF=0.333,.;AA=T;DB	GT	2	1	./.
+20	1110696	.	G	A	67	.	NS=2;DP=99;AF=0.333,.;AA=T;DB	GT:DP	2:9	1:9	./.:9