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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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extra newline #42

Closed citizenlee closed 7 years ago

citizenlee commented 7 years ago

Hi, I've been able to align using:

Linux-x64/graphmap align -C -r genome.fa -d 1Dreads.fastq -o chr.sam

However, when I try to create a sorted bam file, I receive "parse error at line X" messages. Going into the sam file, it looks like there are empty new lines between samlines.

Possibly an error in the code that inserts this during output?

citizenlee commented 7 years ago

I can confirm that removal of the empty new lines as such:

awk 'NF' file.sam > file.cleaned.sam

will allow samtools to sort and generate the bam files.

isovic commented 7 years ago

Hi! Which commit are you currently using? There was a recent Issue #33 which reported the same thing. It should be resolved now, but please do let me know if you have the most recent commit and whether it works so that I can inspect in detail.

Thank you for reporting this! Best regards, Ivan.

citizenlee commented 7 years ago

Hi Ivan, I am on commit 817ba03fc19e0fb2076381eb9536ff99240bd468. This should be the latest version - I just pulled it off git earlier this week.

Let me know how else I can help.

Regards,

Henry

On Thu, Nov 10, 2016 at 5:19 AM, Ivan Sovic notifications@github.com wrote:

Hi! Which commit are you currently using? There was a recent Issue #33 https://github.com/isovic/graphmap/issues/33 which reported the same thing. It should be resolved now, but please do let me know if you have the most recent commit and whether it works so that I can inspect in detail.

Thank you for reporting this! Best regards, Ivan.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/isovic/graphmap/issues/42#issuecomment-259653169, or mute the thread https://github.com/notifications/unsubscribe-auth/AJbSiRmLJAgrKBnjL8S-pQJJH5XTUDn0ks5q8u-kgaJpZM4Kr8qC .

isovic commented 7 years ago

Hi,

Indeed there were empty lines when circular alignment was used. This has been fixed for months now, so I'm closing the issue.

Best regards, Ivan.