hammerlab/prohlatype issues and pull requests

#100 - Merge cells lower float accuracy

Pull Request - State: closed - Opened by rleonid over 7 years ago

#99 - Filter power

Pull Request - State: closed - Opened by rleonid over 7 years ago - 2 comments

#99 - Filter power

Pull Request - State: closed - Opened by rleonid over 7 years ago - 2 comments

#98 - Single alleleable

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#98 - Single alleleable

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#97 - Function of alleles

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#97 - Function of alleles

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#96 - Implement banded pass

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#96 - Implement banded pass

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#95 - Check for reverse complement

Pull Request - State: closed - Opened by rleonid over 7 years ago

#95 - Check for reverse complement

Pull Request - State: closed - Opened by rleonid over 7 years ago

#94 - Use custom fixed width bitvectors for allele sets

Pull Request - State: closed - Opened by rleonid over 7 years ago

#94 - Use custom fixed width bitvectors for allele sets

Pull Request - State: closed - Opened by rleonid over 7 years ago

#93 - Purge old graph alignment logic

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#93 - Purge old graph alignment logic

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#92 - Parametric phmm

Pull Request - State: closed - Opened by rleonid over 7 years ago - 1 comment

#91 - Possible mutations

Issue - State: open - Opened by rleonid almost 8 years ago - 2 comments

#91 - Possible mutations

Issue - State: open - Opened by rleonid almost 8 years ago - 2 comments

#90 - Kmer table doesn't scale.

Issue - State: closed - Opened by rleonid almost 8 years ago - 2 comments

#90 - Kmer table doesn't scale.

Issue - State: closed - Opened by rleonid almost 8 years ago - 2 comments

#89 - Specifics

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#89 - Specifics

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#88 - Specific read

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#88 - Specific read

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#87 - Adding padding from reference haplotypes.

Issue - State: open - Opened by rleonid almost 8 years ago

#87 - Adding padding from reference haplotypes.

Issue - State: open - Opened by rleonid almost 8 years ago

#86 - Careful read tracking through pipeline

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#86 - Careful read tracking through pipeline

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#85 - Queued neighbors

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#85 - Queued neighbors

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#84 - Travis test new cfstream build

Pull Request - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#84 - Travis test new cfstream build

Pull Request - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#83 - Write errors to input named file

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#83 - Write errors to input named file

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#82 - Typing errors log should be named by input

Issue - State: closed - Opened by rleonid almost 8 years ago

#82 - Typing errors log should be named by input

Issue - State: closed - Opened by rleonid almost 8 years ago

#81 - Strand neutral

Pull Request - State: closed - Opened by rleonid almost 8 years ago - 3 comments

#80 - Reverse complement Kmer encoding calculation

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment
Labels: Performance

#79 - Array <-> List transforms

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment
Labels: Performance

#79 - Array <-> List transforms

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment
Labels: Performance

#78 - Latest imgt

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#78 - Latest imgt

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#77 - Biological kmers

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#77 - Biological kmers

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#76 - Consider outputting results in HML

Issue - State: open - Opened by hammer almost 8 years ago

#76 - Consider outputting results in HML

Issue - State: open - Opened by hammer almost 8 years ago

#75 - Version depends

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#75 - Version depends

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#74 - Semi mutable

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#74 - Semi mutable

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#73 - Use an Int64 backed bitset implementation

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#73 - Use an Int64 backed bitset implementation

Pull Request - State: closed - Opened by rleonid almost 8 years ago

#72 - Use batteries

Pull Request - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#72 - Use batteries

Pull Request - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#71 - Investigate alternative allele set data structures

Issue - State: closed - Opened by rleonid almost 8 years ago

#71 - Investigate alternative allele set data structures

Issue - State: closed - Opened by rleonid almost 8 years ago

#70 - Benchmark newly filtered UPenn data

Issue - State: closed - Opened by rleonid almost 8 years ago - 3 comments

#70 - Benchmark newly filtered UPenn data

Issue - State: closed - Opened by rleonid almost 8 years ago - 3 comments

#69 - Benchmark prohlatype w/ performance improvements

Issue - State: closed - Opened by hammer almost 8 years ago - 1 comment
Labels: Performance

#69 - Benchmark prohlatype w/ performance improvements

Issue - State: closed - Opened by hammer almost 8 years ago - 1 comment
Labels: Performance

#68 - Faster

Pull Request - State: closed - Opened by rleonid almost 8 years ago - 2 comments

#68 - Faster

Pull Request - State: closed - Opened by rleonid almost 8 years ago - 2 comments

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

Issue - State: closed - Opened by hammer almost 8 years ago - 1 comment

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

Issue - State: closed - Opened by hammer almost 8 years ago - 1 comment

#66 - Fix CI by fixing dependent library versions (ex. biocaml)

Issue - State: closed - Opened by hammer almost 8 years ago

#66 - Fix CI by fixing dependent library versions (ex. biocaml)

Issue - State: closed - Opened by hammer almost 8 years ago

#65 - Normalize the quality

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#65 - Normalize the quality

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#64 - Neighbors

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#63 - Do not preference the default strand

Issue - State: closed - Opened by rleonid almost 8 years ago

#63 - Do not preference the default strand

Issue - State: closed - Opened by rleonid almost 8 years ago

#62 - Ending story

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#62 - Ending story

Issue - State: closed - Opened by rleonid almost 8 years ago - 1 comment

#61 - Try out on long reads

Issue - State: open - Opened by hammer almost 8 years ago - 1 comment

#61 - Try out on long reads

Issue - State: open - Opened by hammer almost 8 years ago - 1 comment

#60 - Edit distance

Pull Request - State: closed - Opened by rleonid about 8 years ago - 2 comments

#60 - Edit distance

Pull Request - State: closed - Opened by rleonid about 8 years ago - 2 comments

#59 - Add a width option to align2fasta

Issue - State: closed - Opened by rleonid about 8 years ago - 1 comment

#59 - Add a width option to align2fasta

Issue - State: closed - Opened by rleonid about 8 years ago - 1 comment

#58 - Align to fasta

Pull Request - State: closed - Opened by rleonid about 8 years ago

#58 - Align to fasta

Pull Request - State: closed - Opened by rleonid about 8 years ago

#57 - Add back_to_fasta utility

Issue - State: closed - Opened by rleonid about 8 years ago

#57 - Add back_to_fasta utility

Issue - State: closed - Opened by rleonid about 8 years ago

#56 - Split up the test environment

Pull Request - State: closed - Opened by rleonid about 8 years ago

#56 - Split up the test environment

Pull Request - State: closed - Opened by rleonid about 8 years ago

#55 - Add test coverage

Pull Request - State: closed - Opened by rleonid about 8 years ago

#55 - Add test coverage

Pull Request - State: closed - Opened by rleonid about 8 years ago

#54 - Use exon edit distance for allele similarity

Issue - State: closed - Opened by rleonid about 8 years ago - 1 comment

#54 - Use exon edit distance for allele similarity

Issue - State: closed - Opened by rleonid about 8 years ago - 1 comment

#53 - Splice variants in merging graphs

Issue - State: open - Opened by rleonid about 8 years ago

#53 - Splice variants in merging graphs

Issue - State: open - Opened by rleonid about 8 years ago

#52 - Add code coverage

Issue - State: closed - Opened by rleonid about 8 years ago

#52 - Add code coverage

Issue - State: closed - Opened by rleonid about 8 years ago

#51 - Split and parallelize the travis tests.

Issue - State: closed - Opened by rleonid about 8 years ago - 1 comment

#51 - Split and parallelize the travis tests.

Issue - State: closed - Opened by rleonid about 8 years ago - 1 comment

#50 - Lazy the fields

Issue - State: closed - Opened by rleonid about 8 years ago - 2 comments
Labels: Performance

#50 - Lazy the fields

Issue - State: closed - Opened by rleonid about 8 years ago - 2 comments
Labels: Performance

#49 - Investigate biological K-mers

Issue - State: closed - Opened by rleonid about 8 years ago - 2 comments

#49 - Investigate biological K-mers

Issue - State: closed - Opened by rleonid about 8 years ago - 2 comments

#48 - Use a priority queue as opposed to min_elt from Map

Issue - State: closed - Opened by rleonid about 8 years ago - 2 comments
Labels: Performance

GitHub / hammerlab/prohlatype issues and pull requests