7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/vcf.5 src/htslib/vcf.5
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-'\" t
-.TH vcf 5 "August 2013" "htslib" "Bioinformatics formats"
-.SH NAME
-vcf \- Variant Call Format
-.\"
-.\" Copyright (C) 2011 Broad Institute.
-.\" Copyright (C) 2013 Genome Research Ltd.
-.\"
-.\" Author: Heng Li <lh3@sanger.ac.uk>
-.\"
-.\" Permission is hereby granted, free of charge, to any person obtaining a
-.\" copy of this software and associated documentation files (the "Software"),
-.\" to deal in the Software without restriction, including without limitation
-.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
-.\" and/or sell copies of the Software, and to permit persons to whom the
-.\" Software is furnished to do so, subject to the following conditions:
-.\"
-.\" The above copyright notice and this permission notice shall be included in
-.\" all copies or substantial portions of the Software.
-.\"
-.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-.\" DEALINGS IN THE SOFTWARE.
-.\"
-.SH DESCRIPTION
-The Variant Call Format (VCF) is a TAB-delimited format with each data line
-consisting of the following fields:
-.TS
-nlbl.
-1	CHROM	CHROMosome name
-2	POS	the left-most POSition of the variant
-3	ID	unique variant IDentifier
-4	REF	the REFerence allele
-5	ALT	the ALTernate allele(s) (comma-separated)
-6	QUAL	variant/reference QUALity
-7	FILTER	FILTERs applied
-8	INFO	INFOrmation related to the variant (semicolon-separated)
-9	FORMAT	FORMAT of the genotype fields (optional; colon-separated)
-10+	SAMPLE	SAMPLE genotypes and per-sample information (optional)
-.TE
-.P
-The following table gives the \fBINFO\fP tags used by samtools and bcftools.
-.TP
-.B AF1
-Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
-(double)
-.TP
-.B DP
-Raw read depth (without quality filtering)
-(int)
-.TP
-.B DP4
-# high-quality reference forward bases, ref reverse, alternate for and alt rev bases
-(int[4])
-.TP
-.B FQ
-Consensus quality. Positive: sample genotypes different; negative: otherwise
-(int)
-.TP
-.B MQ
-Root-Mean-Square mapping quality of covering reads
-(int)
-.TP
-.B PC2
-Phred probability of AF in group1 samples being larger (,smaller) than in group2
-(int[2])
-.TP
-.B PCHI2
-Posterior weighted chi^2 P-value between group1 and group2 samples
-(double)
-.TP
-.B PV4
-P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
-(double[4])
-.TP
-.B QCHI2
-Phred-scaled PCHI2
-(int)
-.TP
-.B RP
-# permutations yielding a smaller PCHI2
-(int)
-.TP
-.B CLR
-Phred log ratio of genotype likelihoods with and without the trio/pair constraint
-(int)
-.TP
-.B UGT
-Most probable genotype configuration without the trio constraint
-(string)
-.TP
-.B CGT
-Most probable configuration with the trio constraint
-(string)
-.TP
-.B VDB
-Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites
-(float)
-.TP
-.B RPB
-Mann-Whitney rank-sum test for tail distance bias
-(float)
-.TP
-.B HWE
-Hardy-Weinberg equilibrium test (Wigginton et al)
-(float)
-.P
-.SH SEE ALSO
-.TP
-https://github.com/samtools/hts-specs
-The full VCF/BCF file format specification
-.TP
-.I A note on exact tests of Hardy-Weinberg equilibrium
-Wigginton JE et al
-PMID:15789306
-.\" (http://www.ncbi.nlm.nih.gov/pubmed/15789306)