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First working version #5

Merged
merged 155 commits into from
Jan 7, 2021
Merged

First working version #5

merged 155 commits into from
Jan 7, 2021

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murphycj2
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@murphycj2
init classes
029a578
@murphycj2
common args
8a11288
@murphycj2
add some util functions
d6cd47a
@murphycj2
very basic cli finished
f7b6c54
@murphycj2
some cli error checking
da48a87
@murphycj2
parse sample info
a514d80
@murphycj2
rename a arg
9801756
@murphycj2
some commetns
684870e
@murphycj2
add vcf option
2bf914b
@murphycj2
parse vcf
3ab9168
@murphycj2
automated search for sample bam file
3ba80a6
@murphycj2
basic extraction module
d5e2992
@murphycj2
add some options
b68ee17
@murphycj2
standardize sex nomeclature
0b4c00a
@murphycj2
some bug fixes to get extract to work
9e538ed
@murphycj2
add fasta file as option
ab7031a
@murphycj2
add overwrite options
06b12df
@murphycj2
store more data in the extraction data
ae85b39
@murphycj2
pre compute minor allele freq
eb88569
@murphycj2
ignore ds store files
b7be49d
@murphycj2
extract return samples
c5132e0
@murphycj2
get genotyp info per pileup site
bdf0183
@murphycj2
bug fix
bd214c9
@murphycj2
store metrics in sampel class
20858fa
@murphycj2
initial minor contamination computation
606f5b1
@murphycj2
basic major contamination
9d15ee1
@murphycj2
cleaning up of minor contamination
71bb270
@murphycj2
cleanup extract and add min coverage
c1b8c93
@murphycj2
remove title file input, change patient to group
d2fbfab
@murphycj2
make cli the entry point, some bug fixes for unittesting
08a678f
@murphycj2 murphycj2 requested a review from rhshah January 6, 2021 22:59
@lgtm-com
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lgtm-com bot commented Jan 6, 2021

This pull request introduces 3 alerts when merging fd4bcb3 into 24a5a0f - view on LGTM.com

new alerts:

  • 2 for Unused local variable
  • 1 for Use of the return value of a procedure

@lgtm-com
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lgtm-com bot commented Jan 7, 2021

This pull request introduces 3 alerts when merging 9a44f2e into 24a5a0f - view on LGTM.com

new alerts:

  • 2 for Unused local variable
  • 1 for Use of the return value of a procedure

@murphycj2 murphycj2 merged commit 791b883 into develop Jan 7, 2021
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@rhshah rhshah rhshah approved these changes

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2 participants
@murphycj2 @rhshah