Fix the weird output behavior of fastq-sample.

[fastq-tools.git] / doc / fastq-sample.1

diff --git a/doc/fastq-sample.1 b/doc/fastq-sample.1
index 53434e037bcad92aa479e8cb01dfc3746e589cf2..0ec7d7273e4c9fb420282c6515a0c73fe9a3eabe 100644 (file)
--- a/doc/fastq-sample.1
+++ b/doc/fastq-sample.1
@@ -4,7 +4,7 @@
 fastq-sample - sample random reads from a fastq file
 
 .SH SYNOPSIS
-.B fastq-sample [OPTION]... [[FILE] [FILE2]]
+.B fastq-sample [OPTION]... FILE [FILE2]
 
 .SH DESCRIPTION
 Given a FASTQ file, random reads are sampled and output, with or without
@@ -28,11 +28,19 @@ sampling with replacement, this number may be greater than 1.0.
 \fB\-o\fR, \fB\-\-output=PREFIX\fR
 The filename prefix to which output should be written. If single-end data is
 being sampled, the output file is [PREFIX].fastq, and with paired-end,
-[PREFIX].1.fastq and [PREFIX].2.fastq.
+[PREFIX].1.fastq and [PREFIX].2.fastq. (Default: \"sample\")
 .TP
 \fB\-r\fR, \fB\-\-with\-replacement\fR
 Sample with replacement. (By default, sampling is done without replacement.)
 .TP
+\fB\-c\fR, \fB\-\-complement-output=PREFIX\fR
+Output reads not included in the random sample to a file (or files) with the
+given prefix. By default, these reads are not output.
+.TP
+\fB\-s\fR, \fB\-\-seed\fR
+Seed the random number generator. Using the same seed on the same data set will
+produce the same random sample.
+.TP
 \fB\-h\fR, \fB\-\-help\fR
 Output a help message and exit.
 .TP