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

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-'\" t
-.TH faidx 5 "August 2015" "htslib" "Bioinformatics formats"
-.SH NAME
-faidx \- an index enabling random access to FASTA files
-.\"
-.\" Copyright (C) 2013, 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
-.IR file.fa .fai,
-.IR file.fasta .fai
-.SH DESCRIPTION
-Using an \fBfai index\fP file in conjunction with a FASTA file containing
-reference sequences enables efficient access to arbitrary regions within
-those reference sequences.
-The index file typically has the same filename as the corresponding FASTA
-file, with \fB.fai\fP appended.
-.P
-An \fBfai index\fP file is a text file consisting of lines each with
-five TAB-delimited columns:
-.TS
-lbl.
-NAME	Name of this reference sequence
-LENGTH	Total length of this reference sequence, in bases
-OFFSET	Offset within the FASTA file of this sequence's first base
-LINEBASES	The number of bases on each line
-LINEWIDTH	The number of bytes in each line, including the newline
-.TE
-.P
-The \fBNAME\fP and \fBLENGTH\fP columns contain the same
-data as would appear in the \fBSN\fP and \fBLN\fP fields of a
-SAM \fB@SQ\fP header for the same reference sequence.
-.P
-The \fBOFFSET\fP column contains the offset within the FASTA file, in bytes
-starting from zero, of the first base of this reference sequence, i.e., of
-the character following the newline at the end of the "\fB>\fP" header line.
-Typically the lines of a \fBfai index\fP file appear in the order in which the
-reference sequences appear in the FASTA file, so \fB.fai\fP files are typically
-sorted according to this column.
-.P
-The \fBLINEBASES\fP column contains the number of bases in each of the sequence
-lines that form the body of this reference sequence, apart from the final line
-which may be shorter.
-The \fBLINEWIDTH\fP column contains the number of \fIbytes\fP in each of
-the sequence lines (except perhaps the final line), thus differing from
-\fBLINEBASES\fP in that it also counts the bytes forming the line terminator.
-.SS FASTA Files
-In order to be indexed with \fBsamtools faidx\fP, a FASTA file must be a text
-file of the form
-.LP
-.RS
-.RI > name
-.RI [ description ...]
-.br
-ATGCATGCATGCATGCATGCATGCATGCAT
-.br
-GCATGCATGCATGCATGCATGCATGCATGC
-.br
-ATGCAT
-.br
-.RI > name
-.RI [ description ...]
-.br
-ATGCATGCATGCAT
-.br
-GCATGCATGCATGC
-.br
-[...]
-.RE
-.LP
-In particular, each reference sequence must be "well-formatted", i.e., all
-of its sequence lines must be the same length, apart from the final sequence
-line which may be shorter.
-(While this sequence line length must be the same within each sequence,
-it may vary between different reference sequences in the same FASTA file.)
-.P
-This also means that although the FASTA file may have Unix- or Windows-style
-or other line termination, the newline characters present must be consistent,
-at least within each reference sequence.
-.P
-The \fBsamtools\fP implementation uses the first word of the "\fB>\fP" header
-line text (i.e., up to the first whitespace character, having skipped any
-initial whitespace after the ">") as the \fBNAME\fP column.
-.SH EXAMPLE
-For example, given this FASTA file
-.LP
-.RS
->one
-.br
-ATGCATGCATGCATGCATGCATGCATGCAT
-.br
-GCATGCATGCATGCATGCATGCATGCATGC
-.br
-ATGCAT
-.br
->two another chromosome
-.br
-ATGCATGCATGCAT
-.br
-GCATGCATGCATGC
-.br
-.RE
-.LP
-formatted with Unix-style (LF) line termination, the corresponding fai index
-would be
-.RS
-.TS
-lnnnn.
-one	66	5	30	31
-two	28	98	14	15
-.TE
-.RE
-.LP
-If the FASTA file were formatted with Windows-style (CR-LF) line termination,
-the fai index would be
-.RS
-.TS
-lnnnn.
-one	66	6	30	32
-two	28	103	14	16
-.TE
-.RE
-.SH SEE ALSO
-.IR samtools (1)
-.TP
-http://en.wikipedia.org/wiki/FASTA_format
-Further description of the FASTA format