Code

Init#1

Code

Merged

sndrtj merged 49 commits intomasterLUMC/rna_cd:masterfrom initLUMC/rna_cd:initCopy head branch name to clipboardJan 30, 2019

+1,068-9

Commits

Commits on Dec 31, 2018

• file stubs

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  8c091bb

• process bam file to array

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  0e03103

• train svm model function

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  fa53c5b

Commits on Jan 2, 2019

• offload array generation to bam_process

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  523ca4f

• train cli function

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  e91b7a5

• train cli in setup.py

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  65b8f5d

• use multiprocessing for bam processing

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  aeacaf6

• plot results

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  35e1bf1

• dump model to disk

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  44f3452

• attempt to make contour plot

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  29da7e0

Commits on Jan 4, 2019

• rename package

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  1d41c80

• remove contour attempts, move to separate branch

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  0416b13

• read obj from disk

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  69607eb

• predict from model

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• predict

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  451294c

Commits on Jan 7, 2019

• write predictions to disk

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  ff619ee

• remove confusing plot elements

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  02c5275

• fix flake8 errors

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  c92e8eb

• test stubs

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  5b815b1

Commits on Jan 16, 2019

• add help to train cli

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• help messages for classify cli

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  baed5a3

• install and usages in readme

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  0924e77

Commits on Jan 17, 2019

• utils testing

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  4852d20

Commits on Jan 23, 2019

• some cli testing

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  3ec451d

• add path callback testing

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  f79434d

• train cli errors test

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  0e3ddf7

• add chop contig test

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  5522162

• classify cli errors testing

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  6103152

• add travis yaml

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  2c2c0cd

• fix travis

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  501060f

• fix flake errors

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  c182a12

• add pytest cov to requirements-dev

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  b5f63f0

• reorganize travis yaml

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  83be8b6

• fix coverage?

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  e5c92e9

• fix coverage?

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  3b43b54

• use coverage module directly

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  7ce0418

• reinstate install

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  127af8f

• codecov with travis

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• add badges in readme

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  5b6d83f

Commits on Jan 28, 2019

• fix headers and test python 3.5 as well

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  653ce10

• python requires in setup py

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  9916af9

• unpack tuple and some extra comments

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  42cd785

• unpack more tuples and chance some more names

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  365fde8

• clarification on return types

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  1384de7

• sanity checks on chop contig.

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  07d28bf

• extra docs on callbacks

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  dc00a4e

• docstring on training and extra sanity check on empty lists

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  a8dd866

• more tuple unpacking

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  833b582

• better name for variable

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  fa02ca1