Qsamtofastq

[ChristinaXu2017]

Description

An existing tool is updated, which converts SAM/BAM to FASTQ. It is based on old qpicard::QSamToFastq, below new options are added:

USAGE: QSamToFastq [options]
Options:

...

INCLUDE_SUPPLEMENTARY_READS=Boolean
                              If true, include supplementary alignments in the output.  Support of supplementary
                              alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set
                              to true and there are paired reads with non-primary alignments.  Default value: false.
                              This option can be set to 'null' to clear the default value. Possible values: {true,
                              false} 

MARK_MATE=Boolean             If true, read id will be appended /1 for first of pair and /2 for second of pair. If
                              false, read id will be as same as BAM record id.  Default value: false. This option can be
                              set to 'null' to clear the default value. Possible values: {true, false} 

BASE_NULL_TO_N=Boolean        If true, set 'N' to fastq record base if SAM record missing base sequence; and then set
                              '!' to base quality. If false, read base will be same as BAM record base, often is '*'. 
                              Default value: true. This option can be set to 'null' to clear the default value. Possible
                              values: {true, false} 

MISS_MATE_RESCUE=Boolean      If true, output a pair of fastq record, set base sequence 'N' and base quality '!' to the
                              missing mate record . If false, output one fastq record only if the input SAM record
                              missing mate.  Default value: true. This option can be set to 'null' to clear the default
                              value. Possible values: {true, false} 

LOG_FILE=String
LOG=String                    output a log file.  Default value: qsamtofastq.log. This option can be set to 'null' to
                              clear the default value. 

Fixes # (issue)

Type of change

Please delete options that are not relevant.

• [x] New feature (non-breaking change which adds functionality)

How Has This Been Tested?

1. to run on real data by command line
2. related unit tests are added

Are WDL Updates Required?

No WDL at moment

Checklist:

• [X] My code follows the style guidelines of this project
• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] I have made corresponding changes to the documentation
• [X] My changes generate no new warnings
• [X] I have added tests that prove my fix is effective or that my feature works
• [X] New and existing unit tests pass locally with my changes

[holmeso]

Could you please adjust the description of this PR, as you are modifying an existing tool rather than creating a new one, and maybe highlight the changes you are making.