X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=tabix.1;h=1bd9533d93577db59b6d97e8fcf912637c56b27d;hp=6b6e2d686adf10a4a02a8ae6f8e7780fa86af4c5;hb=HEAD;hpb=bc08e6c2f34c1367d0fe75dd19cedccfab881229

diff --git a/tabix.1 b/tabix.1
index 6b6e2d6..1bd9533 100644
--- 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
@@ -7,7 +7,7 @@ tabix - Generic indexer for TAB-delimited genome position files
 .SH SYNOPSIS
 .PP
 .B bgzip
-.RB [ \-cdh ]
+.RB [ \-cdhB ]
 .RB [ \-b
 .IR virtualOffset ]
 .RB [ \-s
@@ -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 +81,24 @@ 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 -h
+Print the header/meta lines.
+.TP
+.B -B
+The second argument is a BED file. When this option is in use, the input
+file may not be sorted or indexed. The entire input will be read sequentially. Nonetheless,
+with this option, the format of the input must be specificed correctly on the command line.
+.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;