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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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-so functionality is different in dev branch #50

Closed arahuja closed 9 years ago

arahuja commented 9 years ago

Using the -so flag on the dev branch build does not give properly sorted files. This may be more of an issue with samtools than with SNAP, but when I use samtools index on the file output from SNAP with -so flag I get the following error:

[E::hts_idx_push] unsorted positions

On the master branch, I was able to index files without sorting again

bolosky commented 9 years ago

Ravi fixed this in 1.0dev.72.