matsengrp/linearham

Issues

• figure out why output dir has to be under `/linearham`

  #63 opened 5 years ago by scharch
  7

• Failed Quay build from trigger

  #92 opened 2 years ago by jgallowa07
  0

• update readme with newer (?) output files

  #76 opened 2 years ago by psathyrella
  2

• How to handle paired h/l data

  #93 opened 2 years ago by psathyrella
  0

• Add option for less verbose output dir

  #91 opened 2 years ago by psathyrella
  1

• Github Actions & Quay Container building

  #85 opened 2 years ago by jgallowa07
  2

• Use new partis fcn add_seqs_to_line()

  #74 opened 2 years ago by psathyrella
  4

• Cause of huge number of low-probability nodes

  #75 opened 2 years ago by psathyrella
  6

• Branch lengths almost all much larger than hamming distance

  #90 opened 2 years ago by psathyrella
  0

• Inferred ancestral sequences have mutations in ambiguous regions

  #89 opened 2 years ago by psathyrella
  0

• crash in asr/ess script

  #88 opened 2 years ago by psathyrella
  7

• Update Master -> Main

  #86 opened 3 years ago by jgallowa07
  0

• Docker container doesn't build

  #82 opened 3 years ago by matsen
  2

• light chain crash

  #83 opened 3 years ago by psathyrella
  3

• update partis + maybe add --min-cluster-size arg

  #81 opened 3 years ago by psathyrella
  1

• make default tag on quay.io

  #72 opened 5 years ago by psathyrella
  1

• change actions to positional argument

  #71 opened 5 years ago by psathyrella
  0

• NodeList object where it expected a string

  #70 opened 5 years ago by psathyrella
  1

• linearham crashed

  #65 opened 5 years ago by scharch
  7

• SCons not recognizing arguments to linearham?

  #64 opened 5 years ago by scharch
  3

• git describe crashes build

  #68 opened 5 years ago by psathyrella
  1

• remove mention of ubuntu 16.04 from readme

  #66 opened 5 years ago by psathyrella
  4

• Do we really want to use scons?

  #69 opened 5 years ago by psathyrella
  3

• remove dockerhub image

  #67 opened 5 years ago by psathyrella
  1

• Docker runs example and quits

  #62 opened 5 years ago by scharch
  5

• linearham processing failure -- need help interpreting/solving error message

  #58 opened 5 years ago by wfs-lilly
  4

• Can't seem to get linearham to run -- probably an issue understanding inputs

  #57 opened 5 years ago by wfs-lilly
  6

• Add more info to manual

  #50 opened 5 years ago by psathyrella
  1

• Docker image missing mafft

  #55 opened 5 years ago by wfs-lilly
  33

• Add c++ exception when reading null flexbounds

  #51 opened 5 years ago by eharkins
  0

• biological validation data sets

  #46 opened 6 years ago by matsen
  1

• linearham 2.0: the Awakening

  #44 opened 6 years ago by dunleavy005
  4

• Add a simple CLI

  #37 opened 6 years ago by matsen
  0

• Python wrapper which builds an initial tree

  #36 opened 6 years ago by matsen
  2

• Remove matrix copy construction in Smooshable et al constructors?

  #34 opened 6 years ago by matsen
  4

• Viterbi calculations in the NTI region are incorrect

  #32 opened 6 years ago by dunleavy005
  12

• We should be using the Eigen Index type for indexing

  #29 opened 6 years ago by matsen
  1

• Disable copy constructors?

  #28 opened 6 years ago by matsen
  1

• Split test cases into sections?

  #23 opened 6 years ago by matsen
  1

• B-W or stochastic EM?

  #22 opened 6 years ago by matsen
  2

• What do we do with N bases in the middle of a read?

  #19 opened 6 years ago by matsen
  1

• Compare to bcrham

  #35 opened 8 years ago by matsen
  15

• Give germline-encoded Smooshables pointers back to their Germline objects

  #31 opened 6 years ago by matsen
  1

• Designing a Phylo object

  #39 opened 6 years ago by matsen
  19

• fix likelihood calculation

  #42 opened 6 years ago by dunleavy005
  2

• Test creation of [VDJ]Smooshables

  #26 opened 8 years ago by matsen
  1

• Build object to contain all of the HMM information

  #25 opened 8 years ago by matsen
  2

• build an object to contain information from the partis CSV

  #24 opened 8 years ago by matsen
  0

• Get partis SW results into linearham

  #18 opened 8 years ago by matsen
  1

• parse partis yaml and fit into Germline object

  #17 opened 8 years ago by matsen
  1