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

diff --git src/htslib/sam.5 src/htslib/sam.5
deleted file mode 100644
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--- src/htslib/sam.5
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-'\" t
-.TH sam 5 "August 2013" "htslib" "Bioinformatics formats"
-.SH NAME
-sam \- Sequence Alignment/Map file format
-.\"
-.\" Copyright (C) 2009, 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
-Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started
-with the `@' symbol, each alignment line consists of:
-.TS
-nlbl.
-1	QNAME	Query template/pair NAME
-2	FLAG	bitwise FLAG
-3	RNAME	Reference sequence NAME
-4	POS	1-based leftmost POSition/coordinate of clipped sequence
-5	MAPQ	MAPping Quality (Phred-scaled)
-6	CIGAR	extended CIGAR string
-7	MRNM	Mate Reference sequence NaMe (`=' if same as RNAME)
-8	MPOS	1-based Mate POSistion
-9	TLEN	inferred Template LENgth (insert size)
-10	SEQ	query SEQuence on the same strand as the reference
-11	QUAL	query QUALity (ASCII-33 gives the Phred base quality)
-12+	OPT	variable OPTional fields in the format TAG:VTYPE:VALUE
-.TE
-.PP
-Each bit in the FLAG field is defined as:
-.TS
-lcbl.
-0x0001	p	the read is paired in sequencing
-0x0002	P	the read is mapped in a proper pair
-0x0004	u	the query sequence itself is unmapped
-0x0008	U	the mate is unmapped
-0x0010	r	strand of the query (1 for reverse)
-0x0020	R	strand of the mate
-0x0040	1	the read is the first read in a pair
-0x0080	2	the read is the second read in a pair
-0x0100	s	the alignment is not primary
-0x0200	f	the read fails platform/vendor quality checks
-0x0400	d	the read is either a PCR or an optical duplicate
-0x0800	S	the alignment is supplementary
-.TE
-.P
-where the second column gives the string representation of the FLAG field.
-.SH SEE ALSO
-.TP
-https://github.com/samtools/hts-specs
-The full SAM/BAM file format specification