* 0.1.16-dev (r969:252)

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 483467983b5778bbff4a5bee0a8542b893aca75a..c71fc879d8c5f590f71a90cd27f09573b1520e62 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "16 March 2011" "samtools-0.1.14" "Bioinformatics tools"
+.TH samtools 1 "21 April 2011" "samtools-0.1.16" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
@@ -249,6 +249,16 @@ with the header in
 This command is much faster than replacing the header with a
 BAM->SAM->BAM conversion.
 
+.TP
+.B cat
+samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]
+
+Concatenate BAMs. The sequence dictionary of each input BAM must be identical,
+although this command does not check this. This command uses a similar trick
+to
+.B reheader
+which enables fast BAM concatenation.
+
 .TP
 .B sort
 samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
@@ -275,7 +285,7 @@ Approximately the maximum required memory. [500000000]
 
 .TP
 .B merge
-samtools merge [-nur] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...]
+samtools merge [-nur1f] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...]
 
 Merge multiple sorted alignments.
 The header reference lists of all the input BAM files, and the @SQ headers of
@@ -292,6 +302,12 @@ and the headers of other files will be ignored.
 .B OPTIONS:
 .RS
 .TP 8
+.B -1
+Use zlib compression level 1 to comrpess the output
+.TP
+.B -f
+Force to overwrite the output file if present.
+.TP 8
 .BI -h \ FILE
 Use the lines of
 .I FILE
@@ -303,17 +319,18 @@ replacing any header lines that would otherwise be copied from
 is actually in SAM format, though any alignment records it may contain
 are ignored.)
 .TP
+.B -n
+The input alignments are sorted by read names rather than by chromosomal
+coordinates
+.TP
 .BI -R \ STR
 Merge files in the specified region indicated by
 .I STR
+[null]
 .TP
 .B -r
 Attach an RG tag to each alignment. The tag value is inferred from file names.
 .TP
-.B -n
-The input alignments are sorted by read names rather than by chromosomal
-coordinates
-.TP
 .B -u
 Uncompressed BAM output
 .RE