prepare for release 0.1.3

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 6b1879aefcb6166ef22a2206122d10d1ece0f7a0..acd27bce753f5e801baa6e5b355c8b9ca94a43a0 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "28 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
@@ -163,10 +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
@@ -320,21 +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 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