jlanga/exfi

Issues

• Separate filter building and read classification

  #70 opened 4 years ago by mptrsen
  1

• Keep filter info file

  #71 opened 4 years ago by mptrsen
  1

• Some file and tool names in README are wrong

  #69 opened 4 years ago by mptrsen
  0

• When collapsing, exon ids trid:start-end are not being translated into exon_xxxxxx

  #57 opened 6 years ago by jlanga
  0

• Improve the collapse function

  #56 opened 6 years ago by jlanga
  0

• Integrate into Galaxy?

  #58 opened 6 years ago by jlanga
  0

• Fix messages to stderr in build_splice_graph

  #6 opened 6 years ago by jlanga
  0

• Follow 10 simple rules for making reasearch software more robust

  #7 opened 6 years ago by jlanga
  0

• Set up sphinx to create a documentation from the docstrings

  #20 opened 6 years ago by jlanga
  0

• make exfi a single tool

  #26 opened 6 years ago by jlanga
  3

• split-apply-combine

  #53 opened 6 years ago by jlanga
  1

• report a gff

  #27 opened 6 years ago by jlanga
  0

• bbt -> rapmap/salmon/kallisto and split-apply-combine

  #32 opened 6 years ago by jlanga
  0

• use the toolz package

  #48 opened 6 years ago by jlanga
  0

• threading in polish

  #51 opened 6 years ago by jlanga
  0

• memory in polish

  #52 opened 6 years ago by jlanga
  0

• logging in polish

  #50 opened 6 years ago by jlanga
  0

• compose gfa in memory

  #46 opened 6 years ago by jlanga
  1

• build_splice_graph

  #54 opened 7 years ago by jlanga
  1

• read bloom filters twice in build_splice_graph

  #49 opened 7 years ago by jlanga
  1

• Enable --debug to print everything

  #41 opened 7 years ago by jlanga
  1

• Do multiprocessing as described in https://pymotw.com/3/multiprocessing/communication.html

  #42 opened 7 years ago by jlanga
  1

• Add a "done!" to logging

  #39 opened 7 years ago by jlanga
  0

• if threads==1: do map/starmap

  #40 opened 7 years ago by jlanga
  1

• Bio.SeqIO.parse -> Bio.SeqIO.FastaIO.SimpleFastaParser

  #33 opened 7 years ago by jlanga
  0

• Check stdout or file in output

  #5 opened 7 years ago by jlanga
  0

• Compress biobloommaker files as they come out

  #22 opened 7 years ago by jlanga
  1

• baited_bloom: add option to include/exclude pairs

  #23 opened 7 years ago by jlanga
  1

• Compress the resulting Bloom filters

  #24 opened 7 years ago by jlanga
  1

• Compute overlaps even with nonconsecutive exons

  #18 opened 7 years ago by jlanga
  0

• find_exons.py: delete the merge2 step

  #25 opened 7 years ago by jlanga
  0

• add a functionality to use sealer in between small gaps (<10bp)

  #17 opened 7 years ago by jlanga
  1

• use gfapy instead of my functions

  #16 opened 7 years ago by jlanga
  1

• add options to trim sequences

  #1 opened 8 years ago by jlanga
  0

• use sealer to fill gaps left by SNPs

  #3 opened 8 years ago by jlanga
  1

• make -o - send to stdout

  #4 opened 8 years ago by jlanga
  0

• Set up travis-ci

  #2 opened 8 years ago by jlanga
  0