refactor(q3tiled_aligner): allow user to pass in cached ref index map

[holmeso]

Description

Allow user to pass in cached ref index map. This will greatly reduce I/O.

Type of change

Please delete options that are not relevant.

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

How Has This Been Tested?

Existing tests pass. New test introduced.

Are WDL Updates Required?

n/a

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] 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

[ChristinaXu2017]

It is good to move the method loadReferenceIndexMap(String refFile, String refIndexFile) from the sub-method to the top-level method. So reduced the frequency to load the index file. It seems "String refFile" is no longer used in new method getBlatRecordsSWAll(...)

I suggest to change List getBlatRecordsSWAll(String refFile, String refIndexFile, TIntObjectMap<int[]> cache, String sequence, final String name, int tileLength, String originatingMethod, boolean log, boolean recordsMustComeFromChrInName)
to public static List getBlatRecordsSWAll( Map<ChrPosition, LongRange> refIndexMap, TIntObjectMap<int[]> cache, String sequence, final String name, int tileLength, String originatingMethod, boolean log, boolean recordsMustComeFromChrInName)