Picard CollectHsMetrics: adding missing columns

[vdechand]

• This comment contains a description of changes (with reason)
• CHANGELOG.md has been updated

Not all picard CollectHsMetrics output columns can be included in the report. Missing are:

GENOME_SIZE The number of bases in the reference genome used for alignment.
HS_LIBRARY_SIZE The estimated number of unique molecules in the selected part of the library.
HS_PENALTY_100X The "hybrid selection penalty" incurred to get 80% of target bases to 100X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 100X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 100 * HS_PENALTY_100X.
HS_PENALTY_10X  The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 10 * HS_PENALTY_10X.
HS_PENALTY_20X  The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 20 * HS_PENALTY_20X.
HS_PENALTY_30X  The "hybrid selection penalty" incurred to get 80% of target bases to 30X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 30 * HS_PENALTY_30X.
HS_PENALTY_40X  The "hybrid selection penalty" incurred to get 80% of target bases to 40X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 40X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 40 * HS_PENALTY_40X.
HS_PENALTY_50X  The "hybrid selection penalty" incurred to get 80% of target bases to 50X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 50X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 50 * HS_PENALTY_50X.
PCT_TARGET_BASES_100X   The fraction of all target bases achieving 100X or greater coverage.
PCT_TARGET_BASES_10X    The fraction of all target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_1X The fraction of all target bases achieving 1X or greater coverage.
PCT_TARGET_BASES_20X    The fraction of all target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_2X The fraction of all target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_30X    The fraction of all target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_40X    The fraction of all target bases achieving 40X or greater coverage.
PCT_TARGET_BASES_50X    The fraction of all target bases achieving 50X or greater coverage.

[ewels]

Thanks for this! Took me a while to figure out what effect this has, but it's when you're adding custom columns into your report titles, it would throw an error log message and not have any hover description text?

Thanks for the catch 🙏🏻

[vdechand]

Thanks for this! Took me a while to figure out what effect this has, but it's when you're adding custom columns into your report titles, it would throw an error log message and not have any hover description text?

Thanks for the catch 🙏🏻

From what I remember I did not see any error messages at all.
Thanks for accepting my first open source software contribution!