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SeqLib::BamWriter.WriteRecord() seems to be truncating the qname field #33
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That looks like a valid BAM to me, albeit unaligned to a genome. The EDIT: Ignore above, I see what you're saying now, it's missing |
I'm not entirely sure what is causing it for you, but I've just edited a program I made to see if SetQname is truncating but it doesn't seem to be;
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When I create a new bam record, the new bam record seems to truncate the read name at 23 characters. I am using the following code (note that this is part of a larger program; I just stopped it in the middle to check the file quickly):
When I look at the resulting file, I see this:
@hd VN:1.5 SO:queryname
@rg ID:A SM:testNonRef
abcdefghijklmnopqrstuvw 77 * 0 0 * * 0 0 GGGGTGCCCCCAAAGCGGGCCCGTGGGGGCCTCTGGGATGATGATGATGCACCTCGGCCATCCCAATTCGAGGAGGACCTGGCA DGHIIIIIIIIIIHIIIIIHHHIIHIIIGIIIIIIIIIHIIIIIIIIIIIIIIFIIGIIIGIIIIIHHIIIHIIIIIIGIHHII RG:Z:A X?:Z:HISEQ_0537:1:1101:10000:20114#ACGCTC
abcdefghijklmnopqrstuvw 141 * 0 0 * * 0 0 AAGAGAATGAGGGTCAAGGGTCAGGGCCAGAATCACTGTAGGCCACACAGGCTGTACGGGGTGGAAGGGCAGTCCTTTGTAGGA DGHHIIIIIIIHIHHIIIIIIIIIGHIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIGHIIIIIHIHHIIIIIFHFGHHIG RG:Z:A X?:Z:HISEQ_0537:1:1101:10000:20114#ACGCTC
Based on my understanding, the read name should be "abcdefghijklmnopqrstuvwxyz", but it isn't.
Thanks for any help you can give,
Brendan
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