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[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 0108fdc72554e1f03d9a4dc32512f6fe3f572817..77ac869b77e67c793d6d075cd33dba1f3c49680e 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -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
@@ -324,8 +325,6 @@ Text alignment viewer (based on the ncurses library). In the viewer,
 press `?' for help and press `g' to check the alignment start from a
 region in the format like `chr10:10,000,000'.
 
-.RE
-
 .TP
 .B fixmate
 samtools fixmate <in.nameSrt.bam> <out.bam>
@@ -343,8 +342,6 @@ This command
 .B ONLY
 works with FR orientation and requires ISIZE is correctly set.
 
-.RE
-
 .TP
 .B rmdupse
 samtools rmdupse <input.srt.bam> <out.bam>
@@ -352,8 +349,6 @@ samtools rmdupse <input.srt.bam> <out.bam>
 Remove potential duplicates for single-ended reads. This command will
 treat all reads as single-ended even if they are paired in fact.
 
-.RE
-
 .TP
 .B fillmd
 samtools fillmd [-e] <aln.bam> <ref.fasta>