diff bamCompare.xml @ 28:f7712a057440 draft

new bugfix release

--- a/bamCompare.xml	Mon Mar 17 16:23:58 2014 -0400
+++ b/bamCompare.xml	Wed Apr 02 09:15:44 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.5">
+<tool id="deeptools_bamCompare" name="bamCompare" version="@WRAPPER_VERSION@.0">
     <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -191,15 +191,20 @@
 **What it does**
 
 This tool compares two BAM files based on the number of mapped reads. To
-compare the BAM files, the genome is partitioned into bins of equal size,
-the reads are counted for each bin and each BAM file and finally, a summarizing value is reported.
-This value can be the ratio of the number of reads per bin, the log2 of the ratio or the difference.
-This tool can normalize the number of reads on each BAM file using the SES method
-proposed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). Normalization based on read counts is also available. The
-output is either a bedGraph or a bigWig file containing the bin location and
-the resulting comparison values.
-If paired-end reads are present, the fragment
-length reported in the BAM file is used by default.
+compare the BAM files, the genome is partitioned into bins of equal size, then
+the number of reads found in each BAM file is counted for such bins and
+finally a summarizing value is reported. This value can be the ratio of the
+number of reads per bin, the log2 of the ratio or the difference. This tool
+can normalize the number of reads on each BAM file using the SES method
+proposed by Diaz et al. (2012). "Normalization, bias correction, and peak
+calling for ChIP-seq". Statistical applications in genetics and molecular
+biology, 11(3). Normalization based on read counts is also available. The
+output is either a bedgraph or a bigwig file containing the bin location and
+the resulting comparison values. By default, if reads are mated, the fragment
+length reported in the BAM file is used. In the case of paired-end mapping
+each read mate is treated independently to avoid a bias when a mixture of
+concordant and discordant pairs is present. This means that *each end* will be
+extended to match the fragment length.
 
 
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png