X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=samtools.1;h=869feaac02a64b8e49ba531f5bc164b413da9902;hb=60e0a8467ddbd0b89f15d201dcfe10c8796552b2;hp=4b3f75a1926f0c4248f228f6378d2ff06e3e0c77;hpb=6842e4470dcbd381d0893690b7d07344fd08e831;p=samtools.git

diff --git a/samtools.1 b/samtools.1
index 4b3f75a..869feaa 100644
--- 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