Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Added handling for indels within CollectHsMetrics and CollectTargetedPcrMetrics. #1273

Merged
merged 6 commits into from
Feb 1, 2019
Merged

Added handling for indels within CollectHsMetrics and CollectTargetedPcrMetrics. #1273

merged 6 commits into from
Feb 1, 2019

Commits on Jan 23, 2019

  1. Added handling for indels within CollectHsMetrics and CollectTargeted… 

    …PcrMetrics.

When the INCLUDE_INDELS parameter is set to true:
  1. Deletions within reads are treated as covering the reference bases if the preceding base is high quality
  2. Inserted bases are counted as "on-target" but don't contribute coverage to any target base(s)
    @tfenne
    tfenne committed Jan 23, 2019
    Configuration menu
    Copy the full SHA
    7b573c3 View commit details
    Browse the repository at this point in the history

  2. Fix performance regression.

    @tfenne
    tfenne committed Jan 23, 2019
    Configuration menu
    Copy the full SHA
    57bc875 View commit details
    Browse the repository at this point in the history

Commits on Jan 24, 2019

  1. Added test for indel handling in hs metrics.

    @tfenne
    tfenne committed Jan 24, 2019
    Configuration menu
    Copy the full SHA
    7fd7d8f View commit details
    Browse the repository at this point in the history

Commits on Jan 25, 2019

  1. Fixed failing test. FWIW the barclayTest doesn't like it if you use r… 

    …unPicardCommandLine("I=", input) vs. runPicardCommandLine("I=" + input).
    @tfenne
    tfenne committed Jan 25, 2019
    Configuration menu
    Copy the full SHA
    f8d0b66 View commit details
    Browse the repository at this point in the history

Commits on Jan 31, 2019

  1. Apply suggestions from code review 

    Co-Authored-By: tfenne <[email protected]>
    @tfenne
    Yossi Farjoun and tfenne authored Jan 31, 2019
    Configuration menu
    Copy the full SHA
    767de36 View commit details
    Browse the repository at this point in the history

  2. Changes to address yfarjoun's review comments.

    @tfenne
    tfenne committed Jan 31, 2019
    Configuration menu
    Copy the full SHA
    283341e View commit details
    Browse the repository at this point in the history