Picard Exception: "Multiple Samrecord With Read Name..."

Question

[Pavel Senin]

Hi folks:

How to get around that exception?

So, I am iterating over mapped to genome pairs using SAMRecordIterator, and when I am trying to retrieve the mate's SAMRecord by calling readerRight.queryMate(samRecord) I am having that exception:

 net.sf.samtools.SAMFormatException: Multiple SAMRecord with read name HWI-ST314_0082:8:1107:19789:73933#ATCACG for first end.
    at net.sf.samtools.SAMFileReader.queryMate(SAMFileReader.java:474)...

Is there a way to get them all - those mate-pair records - as a collection??

Answer 1

[samsara]

It seems you have multiple reads with same read name. Grep the input file to check those reads.

[Pavel Senin]

well, i do understand that, moreover, i have they names and can get them iterating with a second instance of samiterator, theoretically... just seems to be odd to see that exception and being unable to get ALL of them to deal with in the same loop.