--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/sam.5	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,68 @@
+'\" 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