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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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Sam header #56

Closed citizenlee closed 7 years ago

citizenlee commented 7 years ago

Seems to be an issue with sam headers with commit a697f01.

While converting sam -> bam, receiving many lines of: [sam_read1] reference 'U00096.2' is recognized as '*'.

This did not pop up when using the same fastq data for alignment on commit 817ba03.

isovic commented 7 years ago

You're right - forgot to trim the sequence headers to first space in the new index. Pushed a fix to master, can you test now?

Best regards, Ivan.

citizenlee commented 7 years ago

Works. Thanks very much, Ivan!