2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/96eba6391a06/ Changeset: 96eba6391a06 Branch: next-stable User: jgoecks Date: 2013-08-02 01:38:24 Summary: Fix imports and parentheses spacing. Affected #: 1 file diff -r 208f93f6cdc00c6d866b8029b0f53990ce0bfadc -r 96eba6391a06e7e6230e06208347dfb51a64a1e1 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -13,6 +13,7 @@ from galaxy.util.json import from_json_string from bx.interval_index_file import Indexes from bx.bbi.bigwig_file import BigWigFile +from bx.bbi.bigbed_file import BigBedFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.data_providers.basic import BaseDataProvider from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar @@ -861,14 +862,14 @@ """ Returns an iterator that provides data in the region chrom:start-end """ - start, end = int(start), int(end) + start, end = int( start ), int( end ) orig_data_filename = self.original_dataset.file_name index_filename = self.converted_dataset.file_name # Attempt to open the BAM file with index bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename ) try: - data = bamfile.fetch(start=start, end=end, reference=chrom) + data = bamfile.fetch( start=start, end=end, reference=chrom ) except ValueError, e: # Try alternative chrom naming. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) https://bitbucket.org/galaxy/galaxy-central/commits/5b9ebcc05ea7/ Changeset: 5b9ebcc05ea7 User: jgoecks Date: 2013-08-02 01:38:49 Summary: Automated merge of next-stable branch Affected #: 1 file diff -r 318f84a819ef9d71dbfffa700d93665b596ef440 -r 5b9ebcc05ea7f187c2a2f528f643bfda30756e5b lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -13,6 +13,7 @@ from galaxy.util.json import from_json_string from bx.interval_index_file import Indexes from bx.bbi.bigwig_file import BigWigFile +from bx.bbi.bigbed_file import BigBedFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.data_providers.basic import BaseDataProvider from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar @@ -861,14 +862,14 @@ """ Returns an iterator that provides data in the region chrom:start-end """ - start, end = int(start), int(end) + start, end = int( start ), int( end ) orig_data_filename = self.original_dataset.file_name index_filename = self.converted_dataset.file_name # Attempt to open the BAM file with index bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename ) try: - data = bamfile.fetch(start=start, end=end, reference=chrom) + data = bamfile.fetch( start=start, end=end, reference=chrom ) except ValueError, e: # Try alternative chrom naming. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.