1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/3f2e69afaf8c/ changeset: 3f2e69afaf8c user: jgoecks date: 2012-10-22 19:19:09 summary: Add chromatin interaction datatype to datatypes.conf, fix bug in data chrint data provider, and enable diagonal heat map track. affected #: 3 files

diff -r 9018e5bb4e6e6de8b52683d2377d449b417269af -r 3f2e69afaf8cc02a35373e544ee426d8e2a41672 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -43,6 +43,11 @@ <display file="ucsc/bigwig.xml" /><display file="igb/bigwig.xml" /></datatype> + <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True"> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> + <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + </datatype><!-- MSI added Datatypes --><datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /><!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' --><!-- End MSI added Datatypes -->

diff -r 9018e5bb4e6e6de8b52683d2377d449b417269af -r 3f2e69afaf8cc02a35373e544ee426d8e2a41672 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -1444,7 +1444,7 @@ """ Provides """ - + rval = [] message = None for count, line in enumerate( iterator ): @@ -1484,15 +1484,15 @@ """ """ # Modify start as needed to get earlier interactions with start region. - start = max( 0, int( start) - 1000000 ) + start = max( 0, int( start ) - 1000000 ) def filter( iter ): for line in iter: feature = line.split() - s1 = int( feature[1] ), - e1 = int( feature[2] ), + s1 = int( feature[1] ) + e1 = int( feature[2] ) c = feature[3] - s2 = int( feature[4] ), - e2 = int( feature[5] ), + s2 = int( feature[4] ) + e2 = int( feature[5] ) if ( ( c == chrom ) and ( s1 < end and e1 > start ) and ( s2 < end and e2 > start ) ): yield line return filter( TabixDataProvider.get_iterator( self, chrom, start, end ) )

diff -r 9018e5bb4e6e6de8b52683d2377d449b417269af -r 3f2e69afaf8cc02a35373e544ee426d8e2a41672 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4156,7 +4156,7 @@ "FeatureTrack": FeatureTrack, "VcfTrack": VcfTrack, "ReadTrack": ReadTrack, - // "DiagonalHeatmapTrack": DiagonalHeatmapTrack, + "DiagonalHeatmapTrack": DiagonalHeatmapTrack, "CompositeTrack": CompositeTrack, "DrawableGroup": DrawableGroup };

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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