def _getReadAlignments(self, reference, start, end, readGroupSet,
readGroup):
"""
Returns an iterator over the specified reads
"""
# TODO If reference is None, return against all references,
# including unmapped reads.
samFile = self.getFileHandle(self._dataUrl)
referenceName = reference.getLocalId().encode()
# TODO deal with errors from htslib
start, end = self.sanitizeAlignmentFileFetch(start, end)
readAlignments = samFile.fetch(referenceName, start, end)
for readAlignment in readAlignments:
tags = dict(readAlignment.tags)
if readGroup is None:
if 'RG' in tags:
alignmentReadGroupLocalId = tags['RG']
readGroupCompoundId = datamodel.ReadGroupCompoundId(
readGroupSet.getCompoundId(),
str(alignmentReadGroupLocalId))
yield self.convertReadAlignment(readAlignment, readGroupSet,
str(readGroupCompoundId))
else:
if self._filterReads:
if 'RG' in tags and tags['RG'] == self._localId:
yield self.convertReadAlignment(
readAlignment, readGroupSet,
str(readGroup.getCompoundId()))
else:
yield self.convertReadAlignment(
readAlignment, readGroupSet,
str(readGroup.getCompoundId()))
def testReadGroup(self):
readGroupSet = self.getReadGroupSet()
dataset = readGroupSet.getParentContainer()
localId = "readGroup"
cid = datamodel.ReadGroupCompoundId(readGroupSet.getCompoundId(),
localId)
self.assertRaises(ValueError, datamodel.ReadGroupCompoundId,
readGroupSet.getCompoundId())
self.assertEqual(cid.dataset, dataset.getLocalId())
self.assertEqual(cid.read_group_set, readGroupSet.getLocalId())
self.assertEqual(cid.read_group, localId)
self.assertEqual(cid.dataset_id, dataset.getId())
self.assertEqual(cid.read_group_set_id, readGroupSet.getId())