95 lines
3.8 KiB
Groff
95 lines
3.8 KiB
Groff
|
.TH htsfile 1 "12 September 2024" "htslib-1.21" "Bioinformatics tools"
|
||
|
|
.SH NAME
|
||
|
|
htsfile \- identify high-throughput sequencing data files
|
||
|
|
.\"
|
||
|
|
.\" Copyright (C) 2015, 2017-2018 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 ...
|
||
|
|
.br
|
||
|
|
.B htsfile --copy
|
||
|
|
.RB [ -v ]
|
||
|
|
.I FILE DESTFILE
|
||
|
|
.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
|
||
|
|
Alternatively, when \fB--copy\fR is used, \fBhtsfile\fR takes exactly two
|
||
|
|
arguments and performs a byte-for-byte copy from \fIFILE\fR to \fIDESTFILE\fR.
|
||
|
|
This is similar to \fBcp\fR(1), but HTSlib's remote file access facilities
|
||
|
|
are available for both source and destination.
|
||
|
|
.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.
|
||
|
|
.IP
|
||
|
|
By default, \fB--view\fR refuses to display files in unknown formats.
|
||
|
|
When \fB--verbose\fR is also given, the raw contents of such files are
|
||
|
|
displayed, with non-printable characters shown via C-style "\\x" hexadecimal
|
||
|
|
escape sequences.
|
||
|
|
.TP
|
||
|
|
.BR -C ", " --copy
|
||
|
|
Instead of identifying or displaying the specified files, copy the source
|
||
|
|
\fIFILE\fR to the destination \fIDESTFILE\fR.
|
||
|
|
Only \fB--verbose\fR may be used in conjunction with \fB--copy\fR.
|
||
|
|
.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)
|