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

diff --git src/htslib/htsfile.1 src/htslib/htsfile.1
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-.TH htsfile 1 "15 December 2015" "htslib-1.3" "Bioinformatics tools"
-.SH NAME
-htsfile \- identify high-throughput sequencing data files
-.\"
-.\" Copyright (C) 2015 Genome Research Ltd.
-.\"
-.\" Author: John Marshall <jm18@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 SYNOPSIS
-.B htsfile
-.RB [ -chHv ]
-.IR FILE ...
-.SH DESCRIPTION
-The \fBhtsfile\fR utility attempts to identify what kind of high-throughput
-sequencing data files the specified files are, and provides minimal viewing
-capabilities for some kinds of data file.
-.P
-It can identify sequencing data files such as SAM, BAM, and CRAM;
-variant calling data files such as VCF and BCF;
-index files used to index these data files;
-and compressed versions of many of them.
-.P
-For each \fIFILE\fR given, \fBhtsfile\fP prints a description of the file
-format determined, using similar keyword conventions to \fBfile\fP(1):
-"text" indicates a textual file that can probably be viewed on a terminal;
-"data" indicates binary data;
-"sequence", "variant calling", and "index" indicate different categories of
-data file.
-When it can be identified, the name of the particular file format (such as
-"BAM" or "VCF") is printed at the start of the description.
-.P
-When used to view file contents as text, \fBhtsfile\fP can optionally show
-only headers or only data records, but has no other filtering capabilities.
-Use \fBsamtools\fR or \fBbcftools\fR if you need more extensive viewing or
-filtering capabilities.
-.P
-The following options are accepted:
-.TP 4n
-.BR -c ", " --view
-Instead of identifying the specified files, display a textual representation
-of their contents on standard output.
-.TP
-.BR -h ", " --header-only
-Display data file headers only.
-Implies \fB--view\fR.
-.TP
-.BR -H ", " --no-header
-When viewing files, display data records only.
-.TP
-.BR -v ", " --verbose
-Display additional warnings and diagnostic messages.
-Using \fB--verbose\fR repeatedly further raises the verbosity.
-.PP
-.SH SEE ALSO
-.IR bcftools (1),
-.IR file (1),
-.IR samtools (1)