* samtools-0.1.2-22

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index f7984cc0d0f4af88f015252608e9ecc4afa53159..6b1879aefcb6166ef22a2206122d10d1ece0f7a0 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "23 January 2009" "samtools-0.1.2" "Bioinformatics tools"
+.TH samtools 1 "28 January 2009" "samtools-0.1.2" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
@@ -96,7 +96,7 @@ will be created.
 
 .TP
 .B view
-samtools view [-b] <in.bam> [region1 [...]]
+samtools view [-bhH] <in.bam> [region1 [...]]
 
 Extract/print all or sub alignments in SAM or BAM format. If no region
 is specified, all the alignments will be printed; otherwise only
@@ -110,6 +110,12 @@ format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'.
 .TP 8
 .B -b
 Output in the BAM format.
+.TP
+.B -h
+Include the header in the output.
+.TP
+.B -H
+Output the header only.
 .RE
 
 .TP
@@ -203,7 +209,7 @@ as in the default format we may not know the mapping quality.
 
 .TP
 .B -c
-Call the consensus sequnce using MAQ consensus model. Options
+Call the consensus sequence using MAQ consensus model. Options
 .B -T,
 .B -N
 and
@@ -320,7 +326,7 @@ Reference sequence names and lengths are not acquired from the BAM/SAM header.
 .IP o 2
 CIGAR operations N and P may not be properly handled.
 .IP o 2
-There is a small known memory leak in the viewer.
+There is a small memory leak in the viewer.
 
 .SH AUTHOR
 .PP