modifying picard/hsmetrics.py add target coverage

[carmelinacharalambous]

• This Is regarding the issue raised here . This update adds a new function, _parse_target_coverage(), to the Picard HsMetrics MultiQC module, enabling support for parsing and visualizing per-target coverage metrics from Picard’s hsmetrics_per_target_coverage files.

• GC Bias Plot: Displays normalized coverage versus GC content, helping identify regions with GC-related capture bias.
• Coverage Distribution Plot: Shows the distribution of median-normalized coverage across all target regions to assess uniformity of sequencing.

These plots provide valuable insights into hybrid-capture efficiency and library quality.

• There is example tool output for tool here (Adding input and output html  test-data#350) file name: Sample1_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex_per_target_coverage.txt
• Code is tested and works locally (including with --strict flag)
• Everything that can be represented with a plot instead of a table is a plot
• There aren't any huge tables with > 6 columns (explain reasoning if so)
• Module does not do any significant computational work

[cursor]

Bug: Duplicate Function Definition and Incorrect Usage

The _parse_target_coverage function is defined twice (lines 438 and 498), causing the first definition to be overwritten and unreachable. It's also defined with self but called with module (line 227), and attempts to use self.add_section(), which will fail since it's a standalone function. This appears to be accidentally committed development code.

 

[carmelinacharalambous]

@vladsavelyev Hi Vlad, can I please receive help regarding this PR to hopefully pass the checks and push it to next release please.