1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/346ad6f83be1/ changeset: 346ad6f83be1 branches: user: kanwei date: 2011-06-06 19:17:18 summary: trackster: Fix VCF data provider affected #: 1 file (62 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Jun 06 11:17:31 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Jun 06 13:17:18 2011 -0400 @@ -607,12 +607,12 @@ out.write( line ) out.close() -class VcfDataProvider( TracksDataProvider ): +class VcfDataProvider( TabixDataProvider ): """ VCF data provider for the Galaxy track browser. Payload format: - [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score] + [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score ] """ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } @@ -622,21 +622,20 @@ count = 0 message = None - reader = galaxy_utils.sequence.vcf.Reader( iterator ) - for line in reader: + for line in iterator: if count >= MAX_VALS: message = ERROR_MAX_VALS % "features" break count += 1 feature = line.split() - payload = [ hash(line), vcf_line.pos-1, vcf_line.pos, \ + payload = [ hash(line), int(feature[1])-1, int(feature[1]), # ID: - feature[2], \ + feature[2], # reference base(s): - feature[3], \ + feature[3], # alternative base(s) - feature[4], \ + feature[4], # phred quality score int( feature[5] )] rval.append(payload) 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.