hammerlab/prohlatype

Issues

• Changes to parany.run cause compilation errors

  #151 opened 3 years ago by gltrost
  0

• align2fasta error - "Couldn't extract sequence align date."

  #147 opened 7 years ago by npavlovikj
  17

• a proposal for `src/scripts/run-example-docker.sh`

  #149 opened 6 years ago by biolxy
  1

• Add coverage information to report output

  #128 opened 7 years ago by rleonid
  1

• little bug in the README

  #142 opened 7 years ago by smondet
  2

• Remove polymorphic comparison

  #141 opened 7 years ago by rleonid
  0

• Reorganize code to centralize biological logic in one module

  #111 opened 7 years ago by rleonid
  1

• Use the error type more proactively.

  #112 opened 7 years ago by rleonid
  1

• Standardize versioning logic.

  #117 opened 7 years ago by rleonid
  0

• Check and finalize public facing documentation

  #118 opened 7 years ago by rleonid
  0

• Fix build system to actually have prohlatype lib.

  #116 opened 7 years ago by rleonid
  1

• Remove ".native" from executables

  #119 opened 7 years ago by rleonid
  1

• Integrate json_to_tsv into app structure

  #126 opened 7 years ago by rleonid
  0

• Check splicing logic for all Class I loci.

  #124 opened 7 years ago by rleonid
  2

• Support finer splitting mode

  #123 opened 7 years ago by rleonid
  0

• Implement the overriding prior feature

  #121 opened 7 years ago by rleonid
  0

• Add gap and fold tracking for alignments.

  #44 opened 7 years ago by rleonid
  4

• Use a priority queue as opposed to min_elt from Map

  #48 opened 7 years ago by rleonid
  2

• Lazy the fields

  #50 opened 7 years ago by rleonid
  2

• Add a width option to align2fasta

  #59 opened 7 years ago by rleonid
  1

• Array <-> List transforms

  #79 opened 7 years ago by rleonid
  1

• Ending story

  #62 opened 8 years ago by rleonid
  1

• Neighbors

  #64 opened 8 years ago by rleonid
  1

• Normalize the quality

  #65 opened 8 years ago by rleonid
  1

• Reverse complement Kmer encoding calculation

  #80 opened 8 years ago by rleonid
  1

• Kmer table doesn't scale.

  #90 opened 8 years ago by rleonid
  2

• Careful read tracking through pipeline

  #86 opened 8 years ago by rleonid
  1

• Possible mutations

  #91 opened 8 years ago by rleonid
  2

• Adding padding from reference haplotypes.

  #87 opened 8 years ago by rleonid
  0

• Typing errors log should be named by input

  #82 opened 8 years ago by rleonid
  0

• Investigate alternative allele set data structures

  #71 opened 8 years ago by rleonid
  0

• Investigate biological K-mers

  #49 opened 8 years ago by rleonid
  2

• Fix CI by fixing dependent library versions (ex. biocaml)

  #66 opened 8 years ago by hammer
  0

• Do not preference the default strand

  #63 opened 8 years ago by rleonid
  0

• Consider outputting results in HML

  #76 opened 8 years ago by hammer
  0

• Benchmark newly filtered UPenn data

  #70 opened 8 years ago by rleonid
  3

• Benchmark prohlatype w/ performance improvements

  #69 opened 8 years ago by hammer
  1

• Cache the adjacency calculation.

  #47 opened 8 years ago by rleonid
  1

• Construct canonical filtered read data set so that I can start tuning increasing accuracy in known cases

  #67 opened 8 years ago by hammer
  1

• Use exon edit distance for allele similarity

  #54 opened 8 years ago by rleonid
  1

• Add graph merging functionality

  #43 opened 8 years ago by rleonid
  3

• Expand our benchmark data

  #41 opened 8 years ago by hammer
  2

• Try out on long reads

  #61 opened 8 years ago by hammer
  1

• Add back_to_fasta utility

  #57 opened 8 years ago by rleonid
  0

• Split and parallelize the travis tests.

  #51 opened 8 years ago by rleonid
  1

• Add code coverage

  #52 opened 8 years ago by rleonid
  0

• Splice variants in merging graphs

  #53 opened 8 years ago by rleonid
  0

• Parse the IMGT version

  #40 opened 8 years ago by rleonid
  1

• `make setup` fails

  #24 opened 8 years ago by smondet
  3

• Examine impact of capture kit on WES HLA typing

  #13 opened 9 years ago by hammer
  0