Added support to BED files with DOS end of lines

1.5.13

increased version number to 1.5.13

Fixed issue with sorting bedgraph files

Merge pull request #117 from fidelram/agg_plotting

Use Agg as default plotting backend.

1.5.11

Fixed rare problem with bigwig files that blocked the program execution.

Enhancements of galaxy wrappers

1.5.9.1

Added a fix to bamCorrelate under BED-file mode which was wrongly reducing the size of the BED region to 1.

1.5.9

• Fixed problem with pseudocounts. The original implementation was scaling pseudocounts twice, which resulted in unexpected results for regions with zero reads.
• The tools bigWigCorrelate and bamPEFragmentSize where added to galaxy.
• Added parameter missingDataAsZero to bamCoverage. The default behaviour is unchanged.
• Improved error reporting of bamCorrelate when few bins are computed.

Overall improvements

This release improves the command line installation of deepTools, warning the user when some dependencies are not found.

In regard to the heatmapper we fixed a problem with overlapping labels and overlapping cluster/group names.

Also we changed the default behaviour of computeMatrix to be verbose by default. This is to warn the user of potential problems with the BED regions usually related to duplications and regions with no signal. We also added automatic mapping of chromosome names with and without chr.

For bamCoverage we changed the behavior: now, genome regions without read coverage show a zero. Before, such regions where not part of the bedgraph/bigwig output.

Improved installation, addition of --version to the tools

New in this release:

• Improved installation, now the installation checks if the UCSC dependencies are installed, if not, a message is shown indicating where to get missing programs and pointing the user to the configuration file to edit.
• when running bamCoverage or bamCompare, the system now checks if bedGraphTobigWig is installed, if not, a message is issued and the tools return a bedGraph file instead.
• We added the --version argument to our tools
• A number of bug fixes.

Stable release

For this release we mostly changed the behavior of the heatmapper. Before, the creation of the underlying matrix (a slow process) and the visualization were done together. However, most of the time the visualization required adjustments, for example to try different color combinations. Because of this we separated the creation of the matrix and the plotting of the data. Moreover we added a tool only for plotting a profile. This was also part of the heatmapper before but the number of options was growing too much and we decided it was better to divide the functionality.

Also, we changed the original names of several functions to better reflect their functionality.