From: Daniel Jones <dcjones@cs.washington.edu>
Date: Sun, 9 Dec 2012 21:24:34 +0000 (-0800)
Subject: Man page for fastq-sort. Bump version.
X-Git-Url: https://git.donarmstrong.com/?p=fastq-tools.git;a=commitdiff_plain;h=c2d5b0395937e0b44f55ee1293ab337ba6359af2

Man page for fastq-sort. Bump version.
---

diff --git a/README.md b/README.md
index c906677..b4cff42 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,7 @@ index
 The following programs are provided. See the individual man pages for more
 information.
 
+* *fastq-sort* : sort fastq entries by various keys
 
 * *fastq-grep* : match sequences against regular expressions
 
diff --git a/configure.ac b/configure.ac
index f1e45d9..bdb3024 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,5 +1,5 @@
 
-AC_INIT( [fastq-tools], [0.3], [dcjones@cs.washington.edu] )
+AC_INIT( [fastq-tools], [0.4], [dcjones@cs.washington.edu] )
 AM_INIT_AUTOMAKE( [foreign -Wall -Werror] )
 m4_ifdef([AM_SILENT_RULES],[AM_SILENT_RULES([yes])])
 
diff --git a/doc/Makefile.am b/doc/Makefile.am
index 8695fbd..16f345b 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -1,4 +1,4 @@
 
-dist_man_MANS = fastq-grep.1 fastq-kmers.1 fastq-match.1 fastq-uniq.1 fastq-sample.1
+dist_man_MANS = fastq-grep.1 fastq-kmers.1 fastq-match.1 fastq-uniq.1 fastq-sample.1 fastq-sort.1
 
 
diff --git a/doc/fastq-grep.1 b/doc/fastq-grep.1
index 89bae04..9858553 100644
--- a/doc/fastq-grep.1
+++ b/doc/fastq-grep.1
@@ -11,10 +11,9 @@ Given a PATTERN, specified as a perl-compatible regular expression, print every
 FASTQ entry with a matching nucleotide sequence.
 
 One ore more FILEs may be specified, otherwise input is read from standard input.
-Input files may be gziped.
 
 .SH OPTIONS
-.TP 
+.TP
 \fB\-i\fR, \fB\-\-id\fR
 Match the read ID (by default, the sequence is matched).
 .TP
diff --git a/doc/fastq-sort.1 b/doc/fastq-sort.1
new file mode 100644
index 0000000..7b63ae0
--- /dev/null
+++ b/doc/fastq-sort.1
@@ -0,0 +1,47 @@
+.TH FASTQ-SORT 1
+
+.SH NAME
+fastq-sort - sort entries in a fastq file
+
+.SH SYNOPSIS
+.B fastq-sort [OPTION]... [FILE]...
+
+.SH DESCRIPTION
+Sort a FASTQ file, outputing the sorted file to standard out. If no files are
+given, read from standard input.
+
+.SH OPTIONS
+.TP
+\fB\-r\fR, \fB\-\-reverse\fR
+Sort in reverse (i.e., descending) order.
+.TP
+\fB\-I\fR, \fB\-\-id\fR
+Sort alphabetically by read identifier.
+.TP
+\fB\-S\fR, \fB\-\-seq\fR
+Sort alphabetically by nucleotide sequence.
+.TP
+\fB\-R\fR, \fB\-\-random\fR
+Sort in random order. By default, a fixed seed is used so that random sort is
+deterministic. Use the '--seed' option to produce different random orderings on
+repeated runs.
+.TP
+\fB\-\-seed=[SEED]\fR
+If a decimal integer SEED is given, it is used as the seed when producing a
+random ordering. With no argument, a seed is generated using the current system
+time.
+.TP
+\fB\-G\fR, \fB\-\-gc\fR
+Sort by increasing GC-content.
+.TP
+\fB\-M\fR, \fB\-\-mean-qual\fR
+Sort by increasing mean quality score.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Output a help message and exit.
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Output version information and exit.
+
+.SH AUTHOR
+Written by Daniel C. Jones <dcjones@cs.washington.edu>
diff --git a/src/fastq-sort.c b/src/fastq-sort.c
index c8f8084..3a859bc 100644
--- a/src/fastq-sort.c
+++ b/src/fastq-sort.c
@@ -406,7 +406,7 @@ void print_help()
 "  -R, --random       randomly shuffle the sequences\n"
 "      --seed[=SEED]  seed to use for random shuffle.\n"
 "  -G, --gc           sort by GC content\n"
-"  -M, --mean-qual  sort by median quality score\n" /* TODO */
+"  -M, --mean-qual    sort by median quality score\n"
 "  -h, --help         print this message\n"
 "  -V, --version      output version information and exit\n"
    );