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Major rewrite to enable use of newer pysam, fix several bugs, and add filtering options #104

Merged
merged 105 commits into from
Jun 12, 2019
Merged

Major rewrite to enable use of newer pysam, fix several bugs, and add filtering options #104

merged 105 commits into from
Jun 12, 2019

Commits on Oct 22, 2018

  1. adding min VAF, RNA fragments, and ratio of alt to other nonref

    @iskandr
    iskandr committed Oct 22, 2018
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Commits on Feb 13, 2019

  1. resuming work with new filering options

    @iskandr
    iskandr committed Feb 13, 2019
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  2. fixed test_variant_helpers

    @iskandr
    iskandr committed Feb 13, 2019
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Commits on Feb 16, 2019

  1. trying to get ProteinSequenceGenerator working

    @iskandr
    iskandr committed Feb 16, 2019
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  2. added helper for genomes in tests

    @iskandr
    iskandr committed Feb 16, 2019
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  3. updating tests to use proteinsequencecreator

    @iskandr
    iskandr committed Feb 16, 2019
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Commits on Feb 18, 2019

  1. fixing imports in tests

    @iskandr
    iskandr committed Feb 18, 2019
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  2. renaming variant_sequence_in_reading_frame to VariantORF

    @iskandr
    iskandr committed Feb 18, 2019
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Commits on Feb 21, 2019

  1. finished basic refactoring, now have to figure out why read counts di… 

    …ffer
    @iskandr
    iskandr committed Feb 21, 2019
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  2. figuring out how to get isovar to work with newer pysam

    @iskandr
    iskandr committed Feb 21, 2019
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Commits on Feb 22, 2019

  1. making a unified ReadCreator

    @iskandr
    iskandr committed Feb 22, 2019
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  2. combining LocusReadCreator and AlleleReadCreator into single ReadCreator

    @iskandr
    iskandr committed Feb 22, 2019
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Commits on Feb 23, 2019

  1. updating CLI to work with ReadCreator

    @iskandr
    iskandr committed Feb 23, 2019
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Commits on Mar 4, 2019

  1. working on making LocusRead tests correctly match new base0 coordinat… 

    …e system
    @iskandr
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  2. added default converter for None to str '-'

    @iskandr
    iskandr committed Mar 4, 2019
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  3. working on getting base-0 vs base-1 right in the pysam interacting pa… 

    …rts of ReadCreator
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Commits on Mar 5, 2019

  1. working on subtleties of base0 vs. base1 and reference vs. read loci

    @iskandr
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  2. working on subtleties of base0 vs. base1 and reference vs. read loci

    @iskandr
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  3. don't allow partial end of read alleles for insertions

    @iskandr
    iskandr committed Mar 5, 2019
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  4. got locus tests working again

    @iskandr
    iskandr committed Mar 5, 2019
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Commits on Mar 7, 2019

  1. fixing AlleleRead unit tests

    @iskandr
    iskandr committed Mar 7, 2019
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Commits on Mar 13, 2019

  1. adding VariantSequenceCreator and TranslationCreator

    @iskandr
    iskandr committed Mar 13, 2019
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  2. split out VariantSequenceCreator and TranslationCreator

    @iskandr
    iskandr committed Mar 13, 2019
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Commits on Mar 21, 2019

  1. wrote filtering helper functions on CoverageStats object

    @iskandr
    iskandr committed Mar 21, 2019
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Commits on Mar 25, 2019

  1. added more detail to algorithm description

    @iskandr
    iskandr committed Mar 25, 2019
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Commits on Mar 26, 2019

  1. working on pulled results fields out into own object

    @iskandr
    iskandr committed Mar 26, 2019
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Commits on Mar 27, 2019

  1. added IsovarResult

    @iskandr
    iskandr committed Mar 27, 2019
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  2. getting rid of ProteinSequenceCreator

    @iskandr
    iskandr committed Mar 27, 2019
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Commits on Apr 5, 2019

  1. renamed IsovarResult to VariantResult

    @iskandr
    iskandr committed Apr 5, 2019
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  2. adding more docstrings

    @iskandr
    iskandr committed Apr 5, 2019
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  3. removed nucleotide counts

    @iskandr
    iskandr committed Apr 5, 2019
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Commits on Apr 16, 2019

  1. moved overlapping genes/transcripts to VariantResult

    @iskandr
    iskandr committed Apr 16, 2019
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Commits on Apr 29, 2019

  1. added some docstrings to isovar_result

    @iskandr
    iskandr committed Apr 29, 2019
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Commits on May 7, 2019

  1. working on main Isovar entrypoint

    @iskandr
    iskandr committed May 7, 2019
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  2. updated sort key on ProteinSequence

    @iskandr
    iskandr committed May 7, 2019
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Commits on May 9, 2019

  1. adding protein sequence properties to IsovarResult.to_record()

    @iskandr
    iskandr committed May 9, 2019
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  2. including varcode effect predictions in the IsovarResult

    @iskandr
    iskandr committed May 9, 2019
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  3. moved transcript_id_whitelist onto IsovarResult

    @iskandr
    iskandr committed May 9, 2019
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Commits on May 10, 2019

  1. merged TranslationCreator with ProteinSequenceCreator

    @iskandr
    iskandr committed May 10, 2019
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  2. renamed GroupedAlleleReads to ReadEvidence

    @iskandr
    iskandr committed May 10, 2019
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  3. reorganizing filter settings

    @iskandr
    iskandr committed May 10, 2019
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  4. adding filtering options to Isovar

    @iskandr
    iskandr committed May 10, 2019
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  5. added filtering module

    @iskandr
    iskandr committed May 10, 2019
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  6. moved extra method onto ProteinSequenceCreator

    @iskandr
    iskandr committed May 10, 2019
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  7. added helper which does filter splits

    @iskandr
    iskandr committed May 10, 2019
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Commits on May 11, 2019

  1. merging new and old variant effect code

    @iskandr
    iskandr committed May 11, 2019
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  2. added pandas serialization for IsovarResult objects

    @iskandr
    iskandr committed May 11, 2019
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  3. added test for main entrypoint

    @iskandr
    iskandr committed May 11, 2019
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Commits on May 12, 2019

  1. making entrypoint into a function

    @iskandr
    iskandr committed May 12, 2019
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Commits on May 13, 2019

  1. fixed enough typos to get unit test working

    @iskandr
    iskandr committed May 13, 2019
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Commits on May 14, 2019

  1. expanded import list in init

    @iskandr
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  2. adding methods to match unit tests

    @iskandr
    iskandr committed May 14, 2019
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  3. working on fixing up unit tests

    @iskandr
    iskandr committed May 14, 2019
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  4. more unit test fixes

    @iskandr
    iskandr committed May 14, 2019
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  5. made some properties cached so I can avoid precomputing things in __i… 

    …nit__
    @iskandr
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  6. added filter args and splitting out reference context helpers

    @iskandr
    iskandr committed May 14, 2019
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  7. fixing unit tests and deleting unused code

    @iskandr
    iskandr committed May 14, 2019
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  8. fixed more unit tests

    @iskandr
    iskandr committed May 14, 2019
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  9. working on getting dataframe conversions to work for CLI

    @iskandr
    iskandr committed May 14, 2019
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  10. fixing more unit tests

    @iskandr
    iskandr committed May 14, 2019
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  11. got protein sequence tests working

    @iskandr
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  12. finally got rest of unit tests passing

    @iskandr
    iskandr committed May 14, 2019
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  13. added main CLI entrypoint

    @iskandr
    iskandr committed May 14, 2019
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  14. adding filters to main command

    @iskandr
    iskandr committed May 14, 2019
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  15. actually create DataFrame for results

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    iskandr committed May 14, 2019
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Commits on May 15, 2019

  1. added filter flags, expanded first end-to-end test

    @iskandr
    iskandr committed May 15, 2019
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  2. added main CLI test

    @iskandr
    iskandr committed May 15, 2019
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  3. added helpers to check whether Isovar's protein sequence matched varcode

    @iskandr
    iskandr committed May 15, 2019
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  4. small fixes to isovar result

    @iskandr
    iskandr committed May 15, 2019
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  5. added more properties to result

    @iskandr
    iskandr committed May 15, 2019
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  6. added unit test for types of IsovarResult properties

    @iskandr
    iskandr committed May 15, 2019
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Commits on May 16, 2019

  1. moved filtering code to own module

    @iskandr
    iskandr committed May 16, 2019
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  2. got rid of extra prints

    @iskandr
    iskandr committed May 16, 2019
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  3. added more information to IsovarResult about cDNA sequences

    @iskandr
    iskandr committed May 16, 2019
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  4. added alignment score tests

    @iskandr
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  5. fixed alignment_score

    @iskandr
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  6. got rid of keywords for pysam fetch to make other pysam versions happy

    @iskandr
    iskandr committed May 16, 2019
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  7. fixed unit test data path on travis

    @iskandr
    iskandr committed May 16, 2019
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  8. fixed staticmethod

    @iskandr
    iskandr committed May 16, 2019
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  9. improving README

    @iskandr
    iskandr committed May 16, 2019
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  10. removed integration tests while we're incompatible with Vaxrank

    @iskandr
    iskandr committed May 16, 2019
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  11. expanded README

    @iskandr
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  12. added filter tests

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Commits on May 17, 2019

  1. expanded README

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Commits on May 19, 2019

  1. got rid of unused filter functions

    @iskandr
    iskandr committed May 19, 2019
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  2. removed unused helper functions

    @iskandr
    iskandr committed May 19, 2019
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Commits on Jun 10, 2019

  1. added more comments

    @iskandr
    iskandr committed Jun 10, 2019
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  2. added more comments to README

    @iskandr
    iskandr committed Jun 10, 2019
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  3. experimenting with definition list for extra commands

    @iskandr
    iskandr committed Jun 10, 2019
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  4. trying html in REAMDE

    @iskandr
    iskandr committed Jun 10, 2019
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  5. dl for command list in docs

    @iskandr
    iskandr committed Jun 10, 2019
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  6. removed stars for DL entries at bottom of docs

    @iskandr
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  7. moved sequencing recommendations to the bottom

    @iskandr
    iskandr committed Jun 10, 2019
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  8. added more information to README

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  9. alias 'pass' and 'passes_all_filters'

    @iskandr
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  10. added TOC

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  11. updated names in README

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  12. rename to Internal Design

    @iskandr
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  13. added diagram

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  14. moved diagram to the top

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  15. diagram

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Commits on Jun 11, 2019

  1. slight refactoring of CLI to make it easier for reuse from Vaxrank

    @iskandr
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  2. moved output option out of shared code for CLI args

    @iskandr
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  3. import new CLI helpers in __init__

    @iskandr
    iskandr committed Jun 11, 2019
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  4. added kwargs to helper which creates ArgumentParser

    @iskandr
    iskandr committed Jun 11, 2019
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