--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/htsfile.1	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,71 @@
+.TH htsfile 1 "3 February 2015" "htslib-1.2.1" "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 [ -chH ]
+.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.
+.PP
+.SH SEE ALSO
+.IR bcftools (1),
+.IR file (1),
+.IR samtools (1)