Merge remote branch 'remotes/master/master' into fb-annots

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 4b3f75a1926f0c4248f228f6378d2ff06e3e0c77..869feaac02a64b8e49ba531f5bc164b413da9902 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -353,7 +353,7 @@ 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
@@ -371,6 +371,13 @@ 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