Uploaded samtools_0.1.16-1_amd64.changes.

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index ba323926d83451cf4013c511cf832d6e820a76f9..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
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format


@@ -285,7 +285,7 @@ Approximately the maximum required memory. [500000000]
 
 .TP
 .B merge
 
 .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
 
 Merge multiple sorted alignments.
 The header reference lists of all the input BAM files, and the @SQ headers of


@@ -302,6 +302,12 @@ and the headers of other files will be ignored.
 .B OPTIONS:
 .RS
 .TP 8
 .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
 .BI -h \ FILE
 Use the lines of
 .I FILE


@@ -313,17 +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
 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
 .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
 .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
 .B -u
 Uncompressed BAM output
 .RE