Details
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Type:
Bug
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Status: To-Do (View Workflow)
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Priority:
Critical
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
Description
Looking at the 1/14436308-14438564.bam file from IGBF-1291, there are occurrences of paired reads overlapping each other inappropriately. After extracting reads, issue seems to be with reads occurring multiple times in file or with the bitwise flag where reads have unmapped mates.
For example look at the following read in the file problemReads.sam
HK2WYCCXX160124:2:1205:27417:57846
This read appears three times. Two of the reads are mates to each other (look at column 8) but are not mapped in a proper pair, while the other does not have a mate. When viewed in IGB with show as paired, the pair overlaps other reads.
Might have to do with how IGB renders pairs that are not mapped in proper pair.
