* samtools-0.1.7-14 (r591)

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index dee35abba1fb89c6dae1ec5cb3e5b83ebb92d0fe..b0287791af092cc1175d88f44525a7a3db426437 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "2 September 2009" "samtools-0.1.6" "Bioinformatics tools"
+.TH samtools 1 "10 November 2009" "samtools-0.1.7" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
@@ -123,8 +123,9 @@ is specified, all the alignments will be printed; otherwise only
 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'. The
-coordinate is 1-based.
+format: `chr2' (the whole chr2), `chr2:1000000' (region starting from
+1,000,000bp) or `chr2:1,000,000-2,000,000' (region between 1,000,000 and
+2,000,000bp including the end points). The coordinate is 1-based.
 
 .B OPTIONS:
 .RS
@@ -231,6 +232,8 @@ covering reads, the first alllele, the second allele, # reads supporting
 the first allele, # reads supporting the second allele and # reads
 containing indels different from the top two alleles.
 
+The position of indels is offset by -1.
+
 .B OPTIONS:
 .RS