lilac v1.6

Technical:

• tumor-only mode write fragment into tumor coverage columns instead of ref

Bugs:

• protect against deletion in read near end of coding region

Config:

• in tumor-only mode specify the tumor BAM file with -tumor_bam instead of -reference_bam
• removed 'write_all_files', instead use 'write_types selecting 1 or more from SUMMARY, FRAGMENTS, READS, REF_COUNTS