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Commits on Feb 16, 2020

• Bump version

  pmelsted

  committed
  ae81a86

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Commits on Feb 11, 2020

• Merge branch 'devel' of https://github.com/pachterlab/kallisto into devel

  pmelsted

  committed
  72f406c

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Commits on Jan 30, 2020

• Write transcripts.txt with kallisto pseudo. The row number of the transcript in transcripts.txt matches the number that is contained within the equivalence class matrix.ec, 0-indexed.

  sbooeshaghi

  committed
  e3beeea

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Commits on Dec 16, 2019

• Enables specifying many input files for scRNA-seq technologies. Closes #226.

  pmelsted

  committed
  9f3bc53

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Commits on Dec 13, 2019

• Fixes #240

  pmelsted

  committed
  bb55302

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Commits on Dec 10, 2019

• Makes HDF5 use optional

  pmelsted

  committed
  079a670

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Commits on Nov 20, 2019

• Merge remote-tracking branch 'origin/devel' into devel

  pmelsted

  committed
  e7954e0

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• First working version, tested on 10xv2

  pmelsted

  committed
  eae217b

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Commits on Nov 15, 2019

• Changed 10xv1 barcode umi seq file number and also made explicit the length of the barcode (14) and the UMI (10) which fixes the multi-A bug.

  sbooeshaghi

  committed
  1e0e2b1

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Commits on Nov 8, 2019

• Adds progress information, single cell reads for bus, fixes snakefile

  pmelsted

  committed
  ffc1495

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Commits on Nov 4, 2019

• Bump version

  pmelsted

  committed
  6267f12

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• Merge branch 'bam_single_cell' into HEAD

  pmelsted

  committed
  ca50e48

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Commits on Sep 9, 2019

• changed indropsv3 input files to be consistent with 10x

  

  A. Sina Booeshaghi

  committed
  69c74d3

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• Fixes virtual destructor warning

  pmelsted

  committed
  ddd0fee

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Commits on Sep 5, 2019

• --bam uses flag instead of NH

  laureneliu

  committed
  c4f0de2

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Commits on Sep 4, 2019

• Fixed inDropsv3 indexing

  sbooeshaghi

  committed
  c8c3c56

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Commits on Sep 2, 2019

• fixes htslib temp files

  pmelsted

  committed
  b11c4d1

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• Merge branch 'devel' of https://github.com/pachterlab/kallisto into devel

  pmelsted

  committed
  32b2e63

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• Deals better with no reads pseudoaligning, closes #23 and #186

  pmelsted

  committed
  bd97976

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• 0 length reads are ok, just ignored, closes #135 and #189

  pmelsted

  committed
  64fe837

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Commits on Aug 13, 2019

• Fixed --num option for bus

  laureneliu

  committed
  638fd4a

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Commits on Jul 29, 2019

• Fixed read number in BUS flag, hopefully

  laureneliu

  committed
  71d10f4

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• Fixed read number in BUS flag, hopefully

  laureneliu

  committed
  1d8655f

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• Uncommented extremely important line for outputing read number in BUS flag

  laureneliu

  committed
  1ab5cd4

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Commits on Jul 26, 2019

• htslib for BAM input in BUS mode

  laureneliu

  committed
  b068841

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• Read number in BUS flag as option

  laureneliu

  committed
  7141b81

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Commits on Jul 25, 2019

• Output either NH or read number as BUS flag

  laureneliu

  committed
  29ae2c3

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Commits on Jul 21, 2019

• Updated BUS usage message

  laureneliu

  committed
  0cbc5d1

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• Added other technologies (untested)

  laureneliu

  committed
  e0ef608

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Commits on Jul 20, 2019

• BAM parsing for technologies with 16 bp barcodes followed by 10 bp umis

  laureneliu

  committed
  af72bf1

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Commits on Jul 15, 2019

• Update README.md

  lakigigar

  authored
  ead5803

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Commits on Jul 4, 2019

• Added inDropsv3

  sbooeshaghi

  committed
  3697cde

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Commits on Jun 28, 2019

• Update README.md

  lakigigar

  authored
  fef827f

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Commits on Jun 12, 2019

• syncing bus definitions

  pmelsted

  committed
  b4447c8

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Commits on Jun 11, 2019

• Version bump

  pmelsted

  committed
  b1e85d5

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