update documentation

diff --git a/samtools.1 b/samtools.1
index c4bd77e3e53ca2c26d0bbf58e638105037d79ab2..d111aa6e3b934881720bdf6ccdead704110b1b29 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "21 May 2009" "samtools-0.1.4" "Bioinformatics tools"
+.TH samtools 1 "6 July 2009" "samtools-0.1.5" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
@@ -27,7 +27,20 @@ format. It imports from and exports to the SAM (Sequence
 Alignment/Map) format, does sorting, merging and indexing, and
 allows to retrieve reads in any regions swiftly.
 
+Samtools is designed to work on a stream. It regards an input file `-'
+as the standard input (stdin) and an output file `-' as the standard output
+(stdout). Several commands can thus be combined with Unix pipes. Samtools
+always output warning and error messages to the standard error output (stderr).
+
+Samtools is also able to open a BAM (not SAM) file on a remote FTP server if the BAM
+file name starts with `ftp://'.
+Samtools checks the current working directory for the index file and will
+download the index upon absence. Samtools achieves random FTP file access
+with the `REST' ftp command. It does not retrieve the entire
+alignment file unless it is asked to do so.
+
 .SH COMMANDS AND OPTIONS
+
 .TP 10
 .B import
 samtools import <in.ref_list> <in.sam> <out.bam>
@@ -85,15 +98,16 @@ will be created.
 
 .TP
 .B view
-samtools view [-bhHS] [-t in.refList] [-o output] [-f reqFlag] [-F
-skipFlag] [-q minMapQ] <in.bam> [region1 [...]]
+samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+skipFlag] [-q minMapQ] [-l library] [-r readGroup] <in.bam>|<in.sam> [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
-alignments overlapping with the specified regions will be output. An
+alignments overlapping the specified regions will be output. An
 alignment may be given multiple times if it is overlapping several
 regions. A region can be presented, for example, in the following
-format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'.
+format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. The coordinate
+is 1-based.
 
 .B OPTIONS:
 .RS
@@ -101,6 +115,10 @@ format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'.
 .B -b
 Output in the BAM format.
 .TP
+.B -u
+Output uncompressed BAM. This option saves time spent on compression/decomprssion
+and is thus preferred when the output is piped to another samtools command.
+.TP
 .B -h
 Include the header in the output.
 .TP
@@ -135,6 +153,12 @@ Skip alignments with bits present in INT [0]
 .TP
 .B -q INT
 Skip alignments with MAPQ smaller than INT [0]
+.TP
+.B -l STR
+Only output reads in library STR [null]
+.TP
+.B -r STR
+Only output reads in read group STR [null]
 .RE
 
 .TP
@@ -155,7 +179,7 @@ format.
 .TP
 .B pileup
 samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list]
-[-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
+[-iscgS2] [-T theta] [-N nHap] [-r pairDiffRate] <in.bam>|<in.sam>
 
 Print the alignment in the pileup format. In the pileup format, each
 line represents a genomic position, consisting of chromosome name,
@@ -195,6 +219,10 @@ allele and # reads containing indels different from the top two alleles.
 Print the mapping quality as the last column. This option makes the
 output easier to parse, although this format is not space efficient.
 
+.TP
+.B -S
+The input file is in SAM.
+
 .TP
 .B -i
 Only output pileup lines containing indels.
@@ -206,6 +234,10 @@ The reference sequence in the FASTA format. Index file
 will be created if
 absent.
 
+.TP
+.B -M INT
+Cap mapping quality at INT [60]
+
 .TP
 .B -t FILE
 List of reference names ane sequence lengths, in the format described
@@ -230,11 +262,14 @@ as in the default format we may not know the mapping quality.
 .B -c
 Call the consensus sequence using MAQ consensus model. Options
 .B -T,
-.B -N
+.B -N,
+.B -I
 and
 .B -r
 are only effective when
 .B -c
+or
+.B -g
 is in use.
 
 .TP
@@ -255,6 +290,10 @@ Number of haplotypes in the sample (>=2) [2]
 .B -r FLOAT
 Expected fraction of differences between a pair of haplotypes [0.001]
 
+.TP
+.B -I INT
+Phred probability of an indel in sequencing/prep. [40]
+
 .RE
 
 .TP
@@ -314,8 +353,7 @@ base. Indel caller does not support the = bases at the moment.
 
 .RE
 
-
-.SH SAM FORFAM
+.SH SAM FORMAT
 
 SAM is TAB-delimited. Apart from the header lines, which are started
 with the `@' symbol, each alignment line consists of: