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Feature/mm flag modifier #36

Merged
15 commits merged into from
Mar 7, 2019
Merged

Feature/mm flag modifier #36

15 commits merged into from
Mar 7, 2019

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ghost
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@ghost ghost commented Mar 7, 2019

@keiranmraine Please review addition of mmFlagModifier and associated tests

@ghost ghost requested a review from keiranmraine March 7, 2019 11:16
keiranmraine
keiranmraine suggested changes Mar 7, 2019
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It all looks good but can you edit the help on bwa_mem.pl?

PCAP-core/bin/bwa_mem.pl

Lines 361 to 372 in 61765fb

=item B<-mmqc>
Mark reads as QCFAIL (0x200, 512) using the mismatchQc program, also adds aux tag 'mm:A:Y'.
WARNING:
bwa_mem.pl will exclude all QCFAIL reads from mapping. If a BAM/CRAM file has been created using
this option please ensure that you pre-process the file to remove the flag 512 if you intend to
reprocess based on that output.
e.g.
bammaskflags maskneg=512 auxexists=mm < mmqc.bam > cleaned.bam

Should now indicate use of mmFlagModifier, or do you think we should just embed it automatically?

@ghost ghost requested a review from keiranmraine March 7, 2019 11:39
keiranmraine
keiranmraine reviewed Mar 7, 2019
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keiranmraine
keiranmraine reviewed Mar 7, 2019
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keiranmraine
keiranmraine suggested changes Mar 7, 2019
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2 things to address

@ghost ghost requested a review from keiranmraine March 7, 2019 11:44
keiranmraine
keiranmraine suggested changes Mar 7, 2019
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What about the example command?

PCAP-core/bin/bwa_mem.pl

Line 375 in 1f5329a

bammaskflags maskneg=512 auxexists=mm < mmqc.bam > cleaned.bam

@ghost ghost requested a review from keiranmraine March 7, 2019 11:51
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keiranmraine approved these changes Mar 7, 2019
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👍

@ghost ghost merged commit b1fe68d into develop Mar 7, 2019
@ghost ghost deleted the feature/mmFlagModifier branch March 7, 2019 13:07
This pull request was closed.
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