Merge pull request #30 from leecbaker/master

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 718ac392016705cb758d4cded7eeded2755faff2..118a6e83079bddd9787e89673d64e7a4b1ddd0b3 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -328,7 +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
@@ -346,6 +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