Mercurial > repos > iuc > varscan_mpileup
comparison varscan.py @ 10:db94eadb92c1 draft default tip
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 1232893782204bb041dd6ed46711295cb0bfc03f"
| author | iuc |
|---|---|
| date | Sat, 04 Dec 2021 22:23:16 +0000 |
| parents | e3f170cc4f95 |
| children |
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| 9:e3f170cc4f95 | 10:db94eadb92c1 |
|---|---|
| 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! |