Merge pull request #30 from leecbaker/master

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 98ce9d04d92d3f38c36ef8809962ea155359c38f..118a6e83079bddd9787e89673d64e7a4b1ddd0b3 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "05 July 2011" "samtools-0.1.17" "Bioinformatics tools"
+.TH samtools 1 "2 September 2011" "samtools-0.1.18" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
@@ -69,7 +69,7 @@ format: `chr2' (the whole chr2), `chr2:1000000' (region starting from
 
 .B OPTIONS:
 .RS
-.TP 8
+.TP 10
 .B -b
 Output in the BAM format.
 .TP
@@ -103,6 +103,10 @@ Output reads in read groups listed in
 .I FILE
 [null]
 .TP
+.BI -s \ FLOAT
+Fraction of templates/pairs to subsample; the integer part is treated as the
+seed for the random number generator [-1]
+.TP
 .B -S
 Input is in SAM. If @SQ header lines are absent, the
 .B `-t'
@@ -324,7 +328,7 @@ which enables fast BAM concatenation.
 
 .TP
 .B sort
-samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+samtools sort [-nof] [-m maxMem] <in.bam> <out.prefix>
 
 Sort alignments by leftmost coordinates. File
 .I <out.prefix>.bam
@@ -342,6 +346,13 @@ Output the final alignment to the standard output.
 .B -n
 Sort by read names rather than by chromosomal coordinates
 .TP
+.B -f
+Use
+.I <out.prefix>
+as the full output path and do not append
+.I .bam
+suffix.
+.TP
 .BI -m \ INT
 Approximately the maximum required memory. [500000000]
 .RE