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Commits on Feb 22, 2022

• Update group quota summary script

  TomJKono

  committed
  408058b

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Commits on Jun 10, 2020

• Make the error reporting show 1-based columns instead. Also clean up some syntax.

  TomJKono

  committed
  1c88d89

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• Add some checking for columns with no data and fix gaps in VCF ref field

  TomJKono

  committed
  47b3307

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Commits on Jun 5, 2020

• Fix indel handling

  TomJKono

  committed
  df3398e

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• Fix case for no indels and add some safeguards for python2

  TomJKono

  committed
  90661e4

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Commits on Jun 4, 2020

• Fix error in getting ref base of indels in VCF_from_FASTA_2.py

  TomJKono

  committed
  f010f7b

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• Add new VCF from FASTA script

  TomJKono

  committed
  e8e4ab7

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Commits on Mar 18, 2020

• Add some new scripts

  TomJKono

  committed
  77ac2be

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Commits on Oct 28, 2019

• Update misc utils repo

  TomJKono

  committed
  3526bdf

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Commits on Nov 10, 2016

• Add script to generate BED intervals from filtered coverage data

  TomJKono

  committed
  ca7b91c

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Commits on Nov 4, 2016

• new script for VCF

  pmorrell

  committed
  ed4bd3e

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Commits on Dec 28, 2015

• Add JGI download script

  TomJKono

  committed
  efcdcec

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Commits on Dec 10, 2015

• Update SNP effect predictor to get correct CDS features

  TomJKono

  committed
  dccf4a9

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Commits on Dec 9, 2015

• Fix indentation in VCF_MAF.py

  TomJKono

  committed
  024bbce

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Commits on Nov 7, 2015

• Remove weird whitspace in Strip_BAM.sh

  TomJKono

  committed
  b02e42f

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• Add tests to check for BAM index in Strip_BAM.sh

  

  Tom Kono

  authored and

  Tom Kono

  committed
  a906205

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Commits on Sep 19, 2015

• Update SRA_Fetch.sh to add write permissions to cloned directories

  TomJKono

  committed
  06eee2f

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Commits on Sep 17, 2015

• Fix help message in SRA_Fetch.sh

  TomJKono

  committed
  245b94b

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• Add SRA_Fetch.sh

  TomJKono

  committed
  4a2f49d

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• Delete SRA_Fetch.sh

  TomJKono

  committed
  80c6b4c

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• Fix command quoting for lftp

  TomJKono

  committed
  b52de9c

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• Fix quoting problem in SRA_Fetch.sh

  TomJKono

  committed
  af27f93

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• Update SRA_Fetch.sh usage message

  TomJKono

  committed
  7500735

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• Update README

  TomJKono

  committed
  1b5802b

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• Add SRA_Fetch.sh to download from NCBI SRA

  TomJKono

  committed
  477ac48

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Commits on Sep 9, 2015

• Update README

  TomJKono

  committed
  73a1862

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• Update README

  TomJKono

  committed
  67d68b5

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• Add script to delete all owned MSI jobs

  TomJKono

  committed
  5fe27a8

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Commits on Sep 3, 2015

• Clean up SNP_Effect_Predictor.py

  TomJKono

  committed
  7425f94

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Commits on Aug 17, 2015

• Update .gitignore to exclude .pyc files

  TomJKono

  committed
  a23d88d

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• Fix a typo

  TomJKono

  committed
  4977544

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Commits on Aug 7, 2015

• Fix a complementation error

  TomJKono

  committed
  30a2d8a

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• Update README

  TomJKono

  committed
  ba76c9b

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• Update README

  TomJKono

  committed
  f57d4a0

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• Add a script that reports silent/nonsynonymous for SNPs in a VCF

  TomJKono

  committed
  dafc1ec

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