Mercurial > repos > iuc > ngsutils_bam_filter
comparison filter.py @ 6:2e957d4c4b95 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 585b25e35a97c9a44d7c1ccb013a9e7db6b5319a
author | iuc |
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date | Wed, 30 Jan 2019 05:29:38 -0500 |
parents | 49bf71fbc574 |
children |
comparison
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5:49bf71fbc574 | 6:2e957d4c4b95 |
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334 self.ref = ref | 334 self.ref = ref |
335 | 335 |
336 def filter(self, bam, read): | 336 def filter(self, bam, read): |
337 if not read.is_unmapped: | 337 if not read.is_unmapped: |
338 if bam.getrname(read.tid) == self.ref: | 338 if bam.getrname(read.tid) == self.ref: |
339 return False | 339 return False |
340 return True | 340 return True |
341 | 341 |
342 def __repr__(self): | 342 def __repr__(self): |
343 return 'Excluding: %s' % (self.ref) | 343 return 'Excluding: %s' % (self.ref) |
344 | 344 |
351 self.ref = ref | 351 self.ref = ref |
352 | 352 |
353 def filter(self, bam, read): | 353 def filter(self, bam, read): |
354 if not read.is_unmapped: | 354 if not read.is_unmapped: |
355 if bam.getrname(read.tid) == self.ref: | 355 if bam.getrname(read.tid) == self.ref: |
356 return True | 356 return True |
357 return False | 357 return False |
358 | 358 |
359 def __repr__(self): | 359 def __repr__(self): |
360 return 'Including: %s' % (self.ref) | 360 return 'Including: %s' % (self.ref) |
361 | 361 |