Initial code review of changes for hg38 alt contigs by rnpandya · Pull Request #63 · amplab/snap

rnpandya · 2015-12-09T03:04:00Z

You can generate test files with tests/alttestgen.py (test.fa, test_alts.txt, test.sam).

AmplabJenkins · 2015-12-09T03:07:40Z

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AmplabJenkins · 2015-12-09T22:17:39Z

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AmplabJenkins · 2015-12-09T22:27:35Z

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Conflicts: SNAPLib/BaseAligner.cpp SNAPLib/Genome.h

AmplabJenkins · 2015-12-09T23:52:35Z

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…results

AmplabJenkins · 2016-01-08T18:32:40Z

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AmplabJenkins · 2016-01-08T23:47:43Z

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AmplabJenkins · 2016-01-11T21:24:50Z

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AmplabJenkins · 2016-01-12T18:58:51Z

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AmplabJenkins · 2016-01-12T23:22:47Z

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AmplabJenkins · 2016-01-14T17:37:27Z

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AmplabJenkins · 2016-01-14T18:47:27Z

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rnpandya added 5 commits December 1, 2015 20:16

Alt mapping - initial sketch in single & paired aligner - WIP

8e4786b

Read genome with alts

6fbf18a

Genome index read/write

3046b30

Alt test data generator

a4b492d

Simple test runs

7e09023

rnpandya assigned bolosky Dec 9, 2015

Handle minus strand alt contigs

cb7a567

Allow extra columns in alt map

89a1f92

rnpandya added 2 commits December 9, 2015 15:31

Compile on Linux

42717f9

Merge branch 'master' into alts

ce53004

Conflicts: SNAPLib/BaseAligner.cpp SNAPLib/Genome.h

Compile on Linux

caa7917

Fix windows compile now

5806956

Fix alt index build

75b3361

Coordinate sort of lifted/unlifted index; fix RC handling; secondary …

237186c

…results

Fix lifted index sort

68f90d2

Compile on Linux

6a4bfd8

Calculate bias table for lifted index

e0df34d

rnpandya added 2 commits January 12, 2016 14:49

Cleanup status printing for alt index build

ea14df2

Pre-alloc alt match info

8d12f71

Add parsing options for v38 ref

fa17fff

Fix rc sort, non-large alt index build

919b959

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