prepare for release 0.1.3

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index f7984cc0d0f4af88f015252608e9ecc4afa53159..acd27bce753f5e801baa6e5b355c8b9ca94a43a0 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 "15 April 2009" "samtools-0.1.3" "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
@@ -157,10 +163,9 @@ maximum mapping quality of the reads covering the site will be inserted
 between the `reference base' and the `read bases' columns. An indel
 occupies an additional line. Each indel line consists of chromosome
 name, coordinate, a star, top two high-scoring ins/del sequences, the
-number of reads strongly supporting the first indel, the number of reads
-strongly supporting the second indel, the number of reads that confer
-little information on distinguishing indels and the number of reads that
-contain indels different from the top two ones.
+number of alignments containing the first indel allele, the number of
+alignments containing the second indel allele, and the number of
+alignments containing indels different from the top two alleles.
 
 .B OPTIONS:
 .RS
@@ -203,7 +208,7 @@ 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
@@ -314,21 +319,19 @@ _
 .SH LIMITATIONS
 .PP
 .IP o 2
-In general, more testing is needed to ensure there is no severe bug.
-.IP o 2
 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.
+CIGAR operation P is not properly handled at the moment.
 .IP o 2
-There is a small known memory leak in the viewer.
+The text viewer mysteriously crashes in a very rare case.
 
 .SH AUTHOR
 .PP
-Heng Li from the Sanger Institute is the author of the C version of
-samtools. Bob Handsaker from the Broad Institute implemented the BGZF
-library and Jue Ruan from Beijing Genomics Institute wrote the RAZF
-library. Various people in the 1000Genomes Project contributed to the
-SAM format specification.
+Heng Li from the Sanger Institute wrote the C version of samtools. Bob
+Handsaker from the Broad Institute implemented the BGZF library and Jue
+Ruan from Beijing Genomics Institute wrote the RAZF library. Various
+people in the 1000Genomes Project contributed to the SAM format
+specification.
 
 .SH SEE ALSO
 .PP