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Commits on Jun 26, 2023

• Correct variable name typo

  tbarton-owen

  authored
  6e9c964

Commits on Apr 1, 2022

• Merge pull request #13 from mitoNGS/devel

  Show description for 09eb63c
  clody23

  authored
  09eb63c

Commits on Mar 23, 2022

• Merge pull request #14 from mitoNGS/new_README

  Show description for 9682fa8
  clody23

  authored
  9682fa8

Commits on Mar 22, 2022

• README points to readthedocs

  domenico-simone

  committed
  4fb4c84

Commits on Mar 2, 2022

• more doc string added to functions

  clody23

  committed
  2e7c282

• changes to mtoolbox yaml file. Note GMAP version is not the latest because 2020.10.14 has issues with genome build

  clody23

  committed
  71c7458

• main change: substitute dictionaries with pandas dataframes and add doc strings to functions

  clody23

  committed
  a13efab

• changes to BEDoutput.py

  clody23

  committed
  489f5a2

• changes to mtoolbox yaml file. Note GMAP version is not the latest because 2020.10.14 has issues with genome build

  clody23

  committed
  a440be7

Commits on Feb 16, 2022

• new functions for parsing indels - should be compatible with long-reads as well

  clody23

  committed
  31a81d8

• comment modules likely not needed to initialize conda env

  clody23

  committed
  7fc26dc

Commits on Feb 14, 2022

• substitute function for ins/dels with function already used for long-reads

  clody23

  committed
  589a9ae

• added comments to functions

  clody23

  committed
  81ba563

Commits on Feb 22, 2021

• set MD = 0 if non-canonical string found

  clody23

  committed
  522b9d4

• change modules for installation

  clody23

  committed
  83d6877

Commits on Nov 30, 2020

• trick to solve cases where bam.cov is longer than fasta

  clody23

  committed
  eb70ba2

• changes in install.sh

  clody23

  committed
  7953a5b

Commits on Oct 17, 2020

• Fixed file exist check

  domenico-simone

  committed
  49a55c4

Commits on Oct 16, 2020

• Fixed rule map_nuclear_MT_PE_SE

  Show description for 8f1abbf
  domenico-simone

  committed
  8f1abbf

Commits on Oct 13, 2020

• Added softclipping function to filter out malformed alignments

  Show description for 2063686
  domenico-simone

  committed
  2063686

Commits on Sep 11, 2020

• variant calling: handling merging of one VCF. Fixes #6

  domenico-simone

  committed
  e058ebe

• SE files are cat'd before mapping vs nuclear. Fixes #5

  domenico-simone

  committed
  e76033b

Commits on Aug 26, 2020

• variant_calling.snakefile: fixed function import

  domenico-simone

  committed
  a929f27

• envs/mtoolbox.yaml, added seqtk. Fixes #2

  domenico-simone

  committed
  fd92e07

Commits on Aug 25, 2020

• doc/installation.rst: updates

  domenico-simone

  committed
  c4cb79d

• install.sh: updated alias

  domenico-simone

  committed
  c73fd6f

• install.sh: new alias command

  domenico-simone

  committed
  2eba604

Commits on Aug 24, 2020

• Update install.sh

  domenico-simone

  authored
  6d776ee

Commits on Jul 3, 2020

• Fixed new alignment filtering workflow

  domenico-simone

  committed
  3918a6f

• Function sam_to_ids fixed

  domenico-simone

  committed
  67641c5

• modules/filter_alignments.py: added functions cat_alignment, cat_alignments

  domenico-simone

  committed
  4382614

Commits on Jul 2, 2020

• Fixed function import and keywords

  domenico-simone

  committed
  899a95b

• Fixed keywords

  domenico-simone

  committed
  d2742bb

Commits on Jul 1, 2020

• Fixed keywords

  domenico-simone

  committed
  f7b4e74

• keep_orphans

  domenico-simone

  committed
  54e6610

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