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amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
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sort option -so expected functionality #117

Closed ramcn closed 3 years ago

ramcn commented 6 years ago

Hello,

I am assuming the functionality of -so option is equivalent to samtools sort and trying to use -so option to generate output bam sorted by coordinate as below. But when I use it to create index using samtools I get a failure as alignment is not sorted.

- snap-aligner paired snap-index-dir SRR1586015_1.fastq SRR1586015_2.fastq -t 32 -so -o -bam snap-1x.bam - samtools index snap-1x.bam [bam_index_core] the alignment is not sorted (SRR1586015.3826889): 56024334 > 56024332 in 18-th chr

Please let me know if this is expected behavior or a bug.

Thank you, Ram

bolosky commented 3 years ago

This was fixed a while ago, I no longer remember in which version, but certainly it's OK in 2.0.