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Extended standalone#63

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msahraeian wants to merge 99 commits intopostprocess_dedup_filterbioinform/neusomatic:postprocess_dedup_filterfrom extended_standalonebioinform/neusomatic:extended_standaloneCopy head branch name to clipboard

+4,417-782

Commits

Commits on Mar 6, 2020

• added new scripts for extending standalone features

  

  Sahraeian

  committed
  9e14ec5

Commits on Mar 9, 2020

• fix for dbsnp

  

  Sahraeian

  committed
  8720927

Commits on Mar 11, 2020

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  046b123

Commits on Mar 12, 2020

• fix_extract_ensemble

  

  Sahraeian

  committed
  9cb9960

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  19b8512

• fix dirnames

  

  Sahraeian

  committed
  58ccf62

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  db2312e

Commits on Mar 14, 2020

• small fix

  

  Sahraeian

  committed
  cab5ff7

Commits on Mar 18, 2020

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  c53f74e

Commits on Mar 19, 2020

• fix features

  

  Sahraeian

  committed
  efa4190

Commits on Apr 10, 2020

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  0ed0e83

• fix ensemble

  

  Sahraeian

  committed
  e4be780

Commits on Apr 22, 2020

• backward compatiblity for call.py

  

  Sahraeian

  committed
  8fc8583

Commits on Apr 28, 2020

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  7514b31

Commits on Apr 29, 2020

• few fixes

  

  Sahraeian

  committed
  8e8ec69

• fix format

  

  Sahraeian

  committed
  2a84509

• small fix

  

  Sahraeian

  committed
  5581ba4

• fix for training loss

  

  Sahraeian

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  115d814

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  c848028

• fix for backward compatibility

  

  Sahraeian

  committed
  a3c4f3e

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  55a498e

Commits on Apr 30, 2020

• fix train loss

  

  Sahraeian

  committed
  f9ee725

• Merge branch 'postprocess_dedup_filter' into extended_standalone

  

  Sahraeian

  committed
  b09f5f6

Commits on May 3, 2020

• fix extend_features

  

  Sahraeian

  committed
  26c4ca4

• improve efficiency in extend_features

  

  Sahraeian

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  757dfab

Commits on May 4, 2020

• fix for extend_features

  

  Sahraeian

  committed
  776ddce

Commits on May 5, 2020

• added seq_complexity

  

  Sahraeian

  committed
  15ff4a8

Commits on May 6, 2020

• fix ensemble

  

  Sahraeian

  committed
  2c4f45d

• more efficient LC

  

  Sahraeian

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  e913e83

• small fix

  

  Sahraeian

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  2be51cc

• filter duplicate by default

  

  Sahraeian

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  e9b83da

Commits on May 7, 2020

• switched fisher test

  

  Sahraeian

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  a54be69

Commits on May 9, 2020

• fix seq_complexity

  

  Sahraeian

  committed
  4f6bf57

• fix num fields

  

  Sahraeian

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  dbe9c4a

Commits on May 10, 2020

• zero anns columns added

  

  Sahraeian

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  cb64681

• fix bug in read_info_extractor.py as in somaticseq

  

  Sahraeian

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  97d16f6

Commits on May 12, 2020

• cluster variants for feature extraction

  

  Sahraeian

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  018e87a

• small fix

  

  Sahraeian

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  0e394ff

• record aligned_pairs

  

  Sahraeian

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  3c061b3

• small fix

  

  Sahraeian

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  709b64b

Commits on May 13, 2020

• more efficient read/ref pos match search

  

  Sahraeian

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  12167e1

• input num_splits

  

  Sahraeian

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  ff00be3

• max_cluster size added

  

  Sahraeian

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  366964e

• better memory management for feature extraction

  

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  839cc63

• not to store aligned_pairs

  

  Sahraeian

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  0501883

• small fix

  

  Sahraeian

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  90a68da

Commits on May 15, 2020

• enable custom header

  

  Sahraeian

  committed
  f83b6b5

• fixed a bug

  

  Sahraeian

  committed
  49c809f

• fix bug in region splitting

  

  Sahraeian

  committed
  2f9905b

• small fix

  

  Sahraeian

  committed
  c4f24ac

• small_fix

  

  Sahraeian

  committed
  1ce3935

• small fix

  

  Sahraeian

  committed
  8b29757

• Merge branch 'extended_standalone' into custom_header

  

  Sahraeian

  committed
  654b90a

• small fix

  

  Sahraeian

  committed
  7b0cb75

Commits on May 16, 2020

• enable custom heading

  

  Sahraeian

  committed
  7706c3b

• small fix

  

  Sahraeian

  committed
  27f98c8

Commits on May 17, 2020

• small fix

  

  Sahraeian

  committed
  0bc4655

Commits on May 23, 2020

• small fix

  

  Sahraeian

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  7deb7d6

Commits on May 28, 2020

• small fix

  

  Sahraeian

  committed
  7897df8

Commits on May 31, 2020

• fix ann

  

  Sahraeian

  committed
  8ac67a1

Commits on Jun 5, 2020

• small fix

  

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  607abcd

Commits on Jun 18, 2020

• added callers vcf to tsv

  

  Sahraeian

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  867ba5f

• merge regions for scanning

  

  Sahraeian

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  635341e

Commits on Jun 19, 2020

• bug fixes for call/post

  

  Sahraeian

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  a52d0c2

• fix_bugs

  

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  2094b3e

• updated versions to 0.3.0

  

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  committed
  30ac6cf

• small fix

  

  Sahraeian

  committed
  c2deecb

• small fix

  

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  bad8004

Commits on Jun 20, 2020

• fix test

  

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  97e4864

Commits on Jun 24, 2020

• fix in resolve variants

  

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  fb6ea21

Commits on Jun 25, 2020

• ensemble with internal features

  

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  1bf40b4

• fix resolve

  

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  2471f8e

Commits on Jul 2, 2020

• small fix

  

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  544e2f2

• small fix

  

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  96d2091

Commits on Jul 19, 2020

• repeat extension

  

  Sahraeian

  committed
  fd2a2f7

Commits on Jul 24, 2020

• small fix

  

  Sahraeian

  committed
  cca94c8

Commits on Jul 29, 2020

• improve cpu multi-thread call.py

  

  Sahraeian

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  b4d2bdf

Commits on Jul 30, 2020

• small fix

  

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  a359327

• updated dockerfile

  

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  f6d3174

• updated docker test

  

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  accb759

Commits on Sep 19, 2020

• fix build

  

  Sahraeian

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  9f5d876

Commits on Oct 6, 2020

• small_fix

  

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  e500bf7

Commits on Nov 7, 2020

• force cov_thr

  

  Sahraeian

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  e48e15d

Commits on Nov 9, 2020

• fix max_cov

  

  Sahraeian

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  a96a236

Commits on Dec 6, 2020

• fixed matrices gradual delete

  

  Sahraeian

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  d804742

Commits on Dec 29, 2020

• fix generate_dataset

  

  Sahraeian

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  45fbcd6

Commits on Jan 22, 2021

• fix ensemble rounding

  

  Sahraeian

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  cff3653

Commits on Jan 23, 2021

• reduce disc I/O while calling

  

  Sahraeian

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  603d582

Commits on Jan 26, 2021

• Updated README

  

  Sahraeian

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  d8738f0

• fix README

  

  Sahraeian

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  e8f9f04

Commits on Mar 5, 2021

• added uint16 as an option for input matrices

  

  Sahraeian

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  088c845

• fixed uint16

  

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  47ac4da

Commits on Mar 8, 2021

• added report_all_alleles

  

  Sahraeian

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  d948d08

• added strict_labeling

  

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  798c880

• fixed strict_labeling

  

  Sahraeian

  committed
  cdfc062

• fixed strict_labeling

  

  Sahraeian

  committed
  74a27df

Commits on Mar 10, 2021

• small fix

  

  Sahraeian

  committed
  a2eed5e

• fixed strict_labeling

  

  Sahraeian

  committed
  399b15c

Commits on Mar 11, 2021

• small fix for strict_labeling

  

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  committed
  13c45b7