Mercurial > repos > youngkim > ezbamqc
comparison ezBAMQC/src/htslib/htsfile.1 @ 0:dfa3745e5fd8
Uploaded
| author | youngkim |
|---|---|
| date | Thu, 24 Mar 2016 17:12:52 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:dfa3745e5fd8 |
|---|---|
| 1 .TH htsfile 1 "3 February 2015" "htslib-1.2.1" "Bioinformatics tools" | |
| 2 .SH NAME | |
| 3 htsfile \- identify high-throughput sequencing data files | |
| 4 .\" | |
| 5 .\" Copyright (C) 2015 Genome Research Ltd. | |
| 6 .\" | |
| 7 .\" Author: John Marshall <jm18@sanger.ac.uk> | |
| 8 .\" | |
| 9 .\" Permission is hereby granted, free of charge, to any person obtaining a | |
| 10 .\" copy of this software and associated documentation files (the "Software"), | |
| 11 .\" to deal in the Software without restriction, including without limitation | |
| 12 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense, | |
| 13 .\" and/or sell copies of the Software, and to permit persons to whom the | |
| 14 .\" Software is furnished to do so, subject to the following conditions: | |
| 15 .\" | |
| 16 .\" The above copyright notice and this permission notice shall be included in | |
| 17 .\" all copies or substantial portions of the Software. | |
| 18 .\" | |
| 19 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 20 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 21 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL | |
| 22 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 23 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING | |
| 24 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | |
| 25 .\" DEALINGS IN THE SOFTWARE. | |
| 26 .\" | |
| 27 .SH SYNOPSIS | |
| 28 .B htsfile | |
| 29 .RB [ -chH ] | |
| 30 .IR FILE ... | |
| 31 .SH DESCRIPTION | |
| 32 The \fBhtsfile\fR utility attempts to identify what kind of high-throughput | |
| 33 sequencing data files the specified files are, and provides minimal viewing | |
| 34 capabilities for some kinds of data file. | |
| 35 .P | |
| 36 It can identify sequencing data files such as SAM, BAM, and CRAM; | |
| 37 variant calling data files such as VCF and BCF; | |
| 38 index files used to index these data files; | |
| 39 and compressed versions of many of them. | |
| 40 .P | |
| 41 For each \fIFILE\fR given, \fBhtsfile\fP prints a description of the file | |
| 42 format determined, using similar keyword conventions to \fBfile\fP(1): | |
| 43 "text" indicates a textual file that can probably be viewed on a terminal; | |
| 44 "data" indicates binary data; | |
| 45 "sequence", "variant calling", and "index" indicate different categories of | |
| 46 data file. | |
| 47 When it can be identified, the name of the particular file format (such as | |
| 48 "BAM" or "VCF") is printed at the start of the description. | |
| 49 .P | |
| 50 When used to view file contents as text, \fBhtsfile\fP can optionally show | |
| 51 only headers or only data records, but has no other filtering capabilities. | |
| 52 Use \fBsamtools\fR or \fBbcftools\fR if you need more extensive viewing or | |
| 53 filtering capabilities. | |
| 54 .P | |
| 55 The following options are accepted: | |
| 56 .TP 4n | |
| 57 .BR -c ", " --view | |
| 58 Instead of identifying the specified files, display a textual representation | |
| 59 of their contents on standard output. | |
| 60 .TP | |
| 61 .BR -h ", " --header-only | |
| 62 Display data file headers only. | |
| 63 Implies \fB--view\fR. | |
| 64 .TP | |
| 65 .BR -H ", " --no-header | |
| 66 When viewing files, display data records only. | |
| 67 .PP | |
| 68 .SH SEE ALSO | |
| 69 .IR bcftools (1), | |
| 70 .IR file (1), | |
| 71 .IR samtools (1) |