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Commits on Mar 26, 2024

• Update modisco

  xjyx

  authored
  0761ddd

• Update modisco

  xjyx

  authored
  b785e5d

Commits on Oct 7, 2023

• Merge branch 'main' of https://github.com/jmschrei/tfmodisco-lite

  jmschrei

  committed
  d98aeb1

• RM dependency upper bounds

  jmschrei

  committed
  b824a7d

Commits on Oct 4, 2023

• Merge pull request jmschrei#42 from austintwang/austintwang-patch-1

  Show description for d6716a5
  jmschrei

  authored
  d6716a5

• Fix pattern indexing in convert

  austintwang

  committed
  64778bf

• Fix inconsistent indentation

  austintwang

  committed
  acdec4b

Commits on Oct 3, 2023

• Merge pull request jmschrei#41 from austintwang/austintwang-patch-1

  Show description for ae1d2c9
  jmschrei

  authored
  ae1d2c9

• Merge pull request jmschrei#40 from ivyraine/main

  Show description for 61db920
  jmschrei

  authored
  61db920

Commits on Sep 29, 2023

• Support seqlet position data in modisco convert

  Show description for 798a435
  austintwang

  authored
  798a435

• Fix bug where non-local tomtom binaries would notbe used

  bytewife

  committed
  b95c4c1

Commits on Sep 27, 2023

• Add conda install hint for missing tomtom req

  bytewife

  committed
  c832ccd

• Print useful error message when tomtom is missing

  bytewife

  committed
  5ba4572

Commits on Aug 12, 2023

• Merge pull request jmschrei#35 from matthewfeickert/build/remove-upper-bound-on-requires-python

  Show description for 570535e
  jmschrei

  authored
  570535e

• Merge pull request jmschrei#36 from austintwang/austintwang-patch-1

  Show description for 4e4e321
  jmschrei

  authored
  4e4e321

Commits on Aug 11, 2023

• Display defaults in help output

  Show description for 4d0c7f5
  austintwang

  authored
  4d0c7f5

Commits on Jul 12, 2023

• build: Remove upper bound on requires-python

  Show description for 73c3a57
  matthewfeickert

  authored
  73c3a57

Commits on Jun 9, 2023

• Merge pull request jmschrei#33 from ivyraine/pr_32

  Show description for ae01f6f
  jmschrei

  authored
  ae01f6f

• Add tomtom/ for TOMTOM file output

  bytewife

  committed
  08cce6b

• Fix TOMTOM matrix file-writing, and add report -t flag for it

  bytewife

  committed
  bd36157

• Merge pull request jmschrei#29 from ivyraine/24_seqlet_extract_bed_fasta

  Show description for 94857c9
  jmschrei

  authored
  94857c9

• Updated report.py to save tomtom output at tomtom.tsv

  soumyakundu

  committed
  60f4b44

Commits on Jun 8, 2023

• Use exact chroms provided by user for peak filtering in seqlet-bed and seqlet-fasta

  bytewife

  committed
  f4037e3

• Remove Y chromosome from '*' set in seqlet-bed, meme, seqlet-fasta

  bytewife

  committed
  445a23a

• Refactor seqlet window calculation functions

  bytewife

  committed
  1ba2928

• Fix conceptual typo

  bytewife

  committed
  3c959ab

• Fix CLI help typo

  bytewife

  committed
  0191c4e

• Print meme, seqlet-bed, seqlet-fasta output to stdout by default & make file-writing optional

  bytewife

  committed
  e3c94ff

• Add get_output() to Writer classes and add send IO error

  bytewife

  committed
  b904f3d

• Fix conceptual off-by-one error in BED implementation

  bytewife

  committed
  59c741a

• Fix off-by-one error in FASTA output

  bytewife

  committed
  68c7423

• Remove redundant newlines in FASTA output

  bytewife

  committed
  1774e33

• Fix bug where seqlet-bed output would be incorrect

  bytewife

  committed
  2a5f9e1

• Fix FASTA output to produce correct sequences

  bytewife

  committed
  96d99e0

Commits on Jun 6, 2023

• Fix bug where pos/neg patterning was used for pos/neg strand in seqlet-bed and seqlet-fasta output

  bytewife

  committed
  25421d9

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