Mercurial > repos > iuc > ngsutils_bam_filter

comparison filter.py @ 6:2e957d4c4b95 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 585b25e35a97c9a44d7c1ccb013a9e7db6b5319a
author iuc
date Wed, 30 Jan 2019 05:29:38 -0500
parents 49bf71fbc574
children
comparison
equal deleted inserted replaced
5:49bf71fbc574 6:2e957d4c4b95
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