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More info for missing pair #22
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Closed in release 0.1.23 |
@GregoryFaust I have the same issue here. But what do you mean by "Closed in release 0.1.23"? What do you think of it? Thanks in advance! |
By "Closed in 0.1.23" I mean that I included the requested additional information into the error message for missing mate, namely the chromosome and position of the read that produced the error. Yes, "samtools sort -n -O SAM" or "sambamba sort -n -u -o /dev/stdout | sambamba view -f sam -h" will work to sort output from bwa or any other paired-end read aligner in a way that samblaster can use. |
@vyx-greg-faust Thanks for your explanation and instructions. |
@GregoryFaust ,
I'm trying to track down a problem with grouping reads. The error I get:
samblaster: Can't find first and/or second of pair in sam block of length 1 for id: xxxxx
It would be exceptionally helpful if the error reported the chromosome and position of the read so they could be quickly pulled for examination.
Thank you.
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