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Assess repeat structure #25

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2 tasks done
a-ludi opened this issue May 24, 2018 · 1 comment
Closed
2 tasks done

Assess repeat structure #25

a-ludi opened this issue May 24, 2018 · 1 comment
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enhancement New feature or request
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Pre-Talk in Jena

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a-ludi commented May 24, 2018 •
edited

It is important to account for repetitive regions as they produce ambiguous and unreliable alignments.

Tasks

  • Mask repetitive regions using the self-alignment information
  • Include test case that verifies the benefits of this measure
@a-ludi a-ludi added the enhancement New feature or request label May 24, 2018
@a-ludi a-ludi added this to the Pre-Talk in Jena milestone May 24, 2018
@a-ludi a-ludi self-assigned this May 24, 2018
a-ludi added a commit that referenced this issue May 24, 2018
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assess repeat structure
8774f8f 
- basic algorithm for assessment
- possibility to generate Dazzler mask

issue #25
a-ludi added a commit that referenced this issue May 24, 2018
@a-ludi
filter reads with "weak" anchors
801c3de 
issue #25
a-ludi added a commit that referenced this issue May 24, 2018
@a-ludi
adjusted integration tests
d7c02a9 
- tests fail due to too many misplaced reads in 4/9 pile ups

issue #25
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a-ludi commented May 24, 2018

Basic implementation done. Further improvements will be handled in new issues.

@a-ludi a-ludi closed this as completed May 24, 2018
This was referenced May 24, 2018
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