add exception message to log file

[ChristinaXu2017]

Description

When org.qcmg.qmule.bam.QSamToFastq throws an exception, it only outputs to std but not log file. Here we make minor improve on QSamToFastq:

1. output exception message to log file and return exit status code "1".
2. check SECOND_END_FASTQ before rescuing the record which is missing the pair.
3. update unit test and delete default log file created during unit tests.

Type of change

Please delete options that are not relevant.

• [x] Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

unit test updated, also run on real data

Are WDL Updates Required?

not yet

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