Add option for running Picard MarkDuplicates with -VALIDATION_STRINGENCY LENIENT parameter

[Nicklas Nordborg]

The BAM file produced by the Hisat/2023 pipeline contained an entry with a strange CIGAR string 46M2D13M13I1D2I31M that Picard exits with an error when running the MarkDuplicates step:

SAM validation error: WARNING::ADJACENT_INDEL_IN_CIGAR:Read name A01932:18:HH3GJDRX2:1:2269:23592:30733,
No M or N operator between pair of I operators in CIGAR

It is possible to ignore this by adding -VALIDATION_STRINGENCY LENIENT to the command line.

This can be solved by adding an extra configuration in reggie-config.xml under a named parameter-set, and use a Software item that selects this parameter set. The Software item should NOT be a default software since we always want to try without the LENIENT parameter first.

[Nicklas Nordborg]

In 6969:

References #1440: Add option for running Picard MarkDuplicates with -VALIDATION_STRINGENCY LENIENT parameter

Added a new configuration option to the default reggie-config.xml. The current implementation for parameters-set requires that the whole default entry is replaced, but this will create a lot of duplicated options. The extends-default attribute is intended to be used for combining the named option with the default options. This require changes in the code that read the configuration file and has not yet been implemented.

[Nicklas Nordborg]

In 6970:

Fixes #1440: Add option for running Picard MarkDuplicates with -VALIDATION_STRINGENCY LENIENT parameter

XmlConfig now merge named options with the default option when the extends-default attribute is set to true value.