further cleanup of duplicate @RG tag warning reporting

[bamtools.git] / README

diff --git a/README b/README
index 7de7fd1d2484a4242e567da85a758a90ed0d3cb1..b3bc1eaa16a01a8e420178772247a200fc92bf1d 100644 (file)
--- a/README
+++ b/README
@@ -47,13 +47,16 @@ of features we hope you find useful.
 usage: bamtools [--help] COMMAND [ARGS]
 
 Available bamtools commands:
-       coverage        Prints coverage statistics from the input BAM file      
-       dump            Dump BAM file contents to text output
-       header          Prints BAM header information
-       index           Generates index for BAM file
-       merge           Merge multiple BAM files into single file
-       sort            Sorts the BAM file according to some criteria
-       stats           Prints some basic statistics from the input BAM file
+       convert         Converts between BAM and a number of other formats
+       count           Prints number of alignments in BAM file
+       coverage        Prints coverage statistics from the input BAM file      
+       filter          Filters BAM file(s) by user-specified criteria
+       header          Prints BAM header information
+       index           Generates index for BAM file
+       merge           Merge multiple BAM files into single file
+       sam             Prints the BAM file in SAM (text) format
+       sort            Sorts the BAM file according to some criteria
+       stats           Prints some basic statistics from the input BAM file
 
 See 'bamtools help COMMAND' for more information on a specific command.