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-hdr.out src/htslib/test/test-vcf-hdr.out
new file mode 100644
index 0000000..45588cc
--- /dev/null
+++ src/htslib/test/test-vcf-hdr.out
@@ -0,0 +1,16 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20150126
+##reference=hs37d5
+##phasing=partial
+##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -6.6778 <= x < -0.6832">
+##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -36469.5723">
+##INFO=<ID=TRAILING,Number=.,Type=Integer,Description="This line contains trailing spaces for testing purposes">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GATK,Number=1,Type=String,Description="Genotype as called by GATK. Always a diploid call. All other genotype stats based on this genotype.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype after Personalis post-processing to match detected chromosome counts.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001