Imported Upstream version 0.2.1

[tabix.git] / tabix.1

diff --git a/tabix.1 b/tabix.1
index 6b6e2d686adf10a4a02a8ae6f8e7780fa86af4c5..3b82c766d8059d3f41adf66e2e2b95a040d7b3ef 100644 (file)
--- a/tabix.1
+++ b/tabix.1
@@ -1,4 +1,4 @@
-.TH tabix 1 "2 November 2009" "tabix-0.1.0" "Bioinformatics tools"
+.TH tabix 1 "11 May 2010" "tabix-0.2.0" "Bioinformatics tools"
 .SH NAME
 .PP
 bgzip - Block compression/decompression utility
@@ -15,7 +15,7 @@ tabix - Generic indexer for TAB-delimited genome position files
 .RI [ file ]
 .PP
 .B tabix
-.RB [ \-0 ]
+.RB [ \-0lf ]
 .RB [ \-p
 .R gff|bed|sam|vcf]
 .RB [ \-s
@@ -69,7 +69,8 @@ are all stored in the index file and thus not used in data retrieval. [1]
 Column of start chromosomal position. [4]
 .TP
 .BI "-e " INT
-Column of end chromosomal position. [5]
+Column of end chromosomal position. The end column can be the same as the
+start column. [5]
 .TP
 .BI "-S " INT
 Skip first INT lines in the data file. [0]
@@ -80,10 +81,16 @@ Skip lines started with character CHAR. [#]
 .B -0
 Specify that the position in the data file is 0-based (e.g. UCSC files)
 rather than 1-based.
+.TP
+.B -f
+Force to overwrite the index file if it is present.
+.TP
+.B -l
+List the sequence names stored in the index file.
 .RE
 
 .SH EXAMPLE
-grep -v ^"#" unsorted.gff | sort -k1,1 -k4,4n | bgzip -c > sorted.gff.gz;
+(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
 
 tabix -p gff sorted.gff.gz;