Excluding soft-clipped reads due to dovetailing small fragments or adapter sequence.
Default adapter sequences match the 12bp sequences used by fastqc
Added parameter to limit record processed by calculate metrics input pass
No longer lazily processing inputs to SAMEvidenceSource
Changed VCF4.1 breakend placeholder to uppercase <UNKNOWN>
Merge branch 'master' of https://github.com/d-cameron/idsv

Conflicts:
	src/main/java/au/edu/wehi/idsv/CommandLineProgram.java
	src/main/java/au/edu/wehi/idsv/SoftClipEvidence.java
	src/test/java/au/edu/wehi/idsv/SoftClipEvidenceTest.java