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chrisquince / DESMAN

De novo Extraction of Strains from MetAgeNomes
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support for specifying single copy regions via a bed file given on the command-line #12

Closed koadman closed 7 years ago

chrisquince commented 7 years ago

Aaron there are some conflicts preventing me from merging this:

bwa mem assembly.fa $x1 | samtools view -q40 -S -b - | samtools sort -o - - > ${x}.sort.bam

======= bwa mem assembly.fa x1 x2 | samtools view -q40 -S -b - | samtools sort -o - - > ${x}.sort.bam

I know you discussed the samtools arguments with Johannes, shall I just merge?

On 20 Dec 2016, at 15:43, Aaron Darling notifications@github.com<mailto:notifications@github.com> wrote:

You can view, comment on, or merge this pull request online at:

https://github.com/chrisquince/DESMAN/pull/12

Commit Summary

File Changes

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koadman commented 7 years ago

the upper line, with $x1 has the correct syntax. yes, please merge if you can. or I can delete this pull request, try to merge on my fork, then send another pull request.

chrisquince commented 7 years ago

That should be right…

On 20 Dec 2016, at 16:18, Aaron Darling notifications@github.com<mailto:notifications@github.com> wrote:

the upper line, with $x1 has the correct syntax. yes, please merge if you can. or I can delete this pull request, try to merge on my fork, then send another pull request.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/chrisquince/DESMAN/pull/12#issuecomment-268285890, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AEtbyyAQKn7uWlQrGNWTt2F2-MVc1qSvks5rJ__BgaJpZM4LR-ZO.