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Add new pVACsplice tool #911

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Add new pVACsplice tool #911

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mrichters and others added 30 commits January 23, 2022 18:02
@mrichters
integrating pvacsplice with pvacseq
f91f17f
@mrichters
modifying files to run PvacsplicePipeline()
401fdca
@mrichters
update splice pipeline
dd6844d
@mrichters
add pvacsplice docs
8aab576
@mrichters
add class to input_file_converter.py
d64207b
@mrichters
recent updates
f5327b1
@mrichters
make pvacsplice compatible with multiple epitope lengths
2e2aba9
@mrichters
add coverage filter
194d68b
@mrichters
update splice pipeline & add FastaVariant
38d4960
@atwollam
reformat for indels when combining in pvacsplice
67a49bd
@mrichters
Merge branch 'staging' into staging
8c6dff4
@mrichters
Merge pull request #4 from griffithlab/staging
d2af88d 
Staging update
@mrichters
Merge pull request #5 from atwollam/splice_old_staging_indref
bb9e65b 
Reformat for indels when combining in pvacsplice
@mrichters
make FastaVariant compatible
d950132
@mrichters
Merge branch 'staging' of https://github.com/mrichters/pVACtools into…
f09a951 
… staging
@mrichters
convert variant coordinates to SNV format to match RegTools
599dfb8
@mrichters
Update filtering junctions stategy
e74d9bd
@mrichters
Remove debugging from filter_regtools_results.py
6c2560f
@mrichters
finalize filter junctions and anotate/combine variants steps in splic…
2e666f1 
…e pipeline
@mrichters
retain strand change from str to int in merged_df[strand]
7aa2ce9
@mrichters
add column "fasta index" to combined file for peptide identification
391825d
@mrichters
add tsl to junction pipeline parameters
909988b
@mrichters
modify to catch previous filtering errors
25e1726
@mrichters
de-duplicate peptide kmers in fasta output
c28000d
@mrichters
create tmp dir and add files not needed in final output
e04c73d
@mrichters
Merge remote-tracking branch 'origin/staging' into pvacsplice
a6d2798
@mrichters
make final edits to splice pipeline & updated output_parser.py
960ea73
@atwollam
pvacsplice testing
9003d64
@mrichters
fix combined report error if only 1 epitope length specified
738e3ad
@mrichters
change final combined splice file suffix to _junctions.tsv
61f3e06
@susannasiebert susannasiebert force-pushed the staging branch 4 times, most recently from eaaa821 to 94434f1 Compare May 23, 2024 16:22
@susannasiebert susannasiebert linked an issue May 31, 2024 that may be closed by this pull request
Prefilter pVACseq and pVACsplice on a user-defined list of biotypes #1090
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@susannasiebert susannasiebert susannasiebert requested changes

Requested changes must be addressed to merge this pull request.

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@mrichters @susannasiebert @atwollam