Re: [Seqan-dev] different rID values for bam vs. sam with identical data, bam results in assertion failure due to length of namestore

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Hi Rob,

can you send us a minimal example, i.e. the SAM file with the header and the offending record and its conversion to BAM and a small demo program?

Thanks,

Manuel

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From: rob f [robf123947@gmail.com]
Sent: Saturday, March 08, 2014 11:24 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] different rID values for bam vs. sam with identical data, bam results in assertion failure due to length of namestore

Hopefully this isn't a duplicate. I didn't see a confirmation in the last email. sorry if it is!

I have a sam and bam file from the same data (an alignment to rn5 refseq genes). Oddly enough I didn't get this error when I aligned to ensembl genes.

I am reading the sam/bam files BamStream, but the same error occurs if I drop down to the lower-level Stream<seqan::Bgzf> approach.

I print length(bamStreamIn._nameStore) and each record.rID as it's read in. Here's my output when I use the bam file version of the data:

namestore size 42252
record.rID : 10364
record.rID : 41714
record.rID : 20136
record.rID : 5043
..c/Users/XXXX/shared/seqan-library-1.4.1/include/seqan/bam_io/read_bam.h:208 Assertion failed : static_cast<__uint64>(record.rID) < length(nameStore(context)) was: 43257 >= 42252

Here's the output when I use the sam file:

namestore size 42252
record.rID : 10318
record.rID : 41436
record.rID : 20031
record.rID : 5009
record.rID : 13876
record.rID : 12206
...
(output continues successfully until the end of the file)

Interestingly the namestore size is the same, but the rIDs are different. Any idea why the rIDs are different and what's causing the assertion error? Thanks

-r