Mercurial > repos > iuc > varscan_mpileup

comparison varscan.py @ 8:4c69f367c326 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 1232893782204bb041dd6ed46711295cb0bfc03f"
author iuc
date Sat, 04 Dec 2021 22:21:15 +0000
parents 100090cb4bec
children
comparison
equal deleted inserted replaced
7:100090cb4bec 8:4c69f367c326
356 if self.error: 356 if self.error:
357 msg_header = '"{0}" failed with:\n{1}\n\n'.format( 357 msg_header = '"{0}" failed with:\n{1}\n\n'.format(
358 self.call, self.error 358 self.call, self.error
359 ) 359 )
360 else: 360 else:
361 msg_header = '{0} failed.\n' 361 msg_header = '{0} failed.\nNo further information about this error is available.\n\n'.format(
362 'No further information about this error is available.\n\n'.format(
363 self.call 362 self.call
364 ) 363 )
365 return msg_header + self.message 364 return msg_header + self.message
366 365
367 366
1043 if mmqs_diff < min_mmqs_diff: 1042 if mmqs_diff < min_mmqs_diff:
1044 record.filter.add('MinMMQSdiff') 1043 record.filter.add('MinMMQSdiff')
1045 if mmqs_diff > max_mmqs_diff: 1044 if mmqs_diff > max_mmqs_diff:
1046 record.filter.add('MMQSdiff') 1045 record.filter.add('MMQSdiff')
1047 if ( 1046 if (
1048 1 - 1047 1
1049 alt_stats.avg_clipped_len 1048 - alt_stats.avg_clipped_len
1050 / ref_stats.avg_clipped_len 1049 / ref_stats.avg_clipped_len
1051 ) > max_relative_len_diff: 1050 ) > max_relative_len_diff:
1052 record.filter.add('ReadLenDiff') 1051 record.filter.add('ReadLenDiff')
1053 else: 1052 else:
1054 # No variant-supporting reads for this record! 1053 # No variant-supporting reads for this record!