110.a2ced6c

What's Changed

• update picard version by @ChristinaXu2017 in #282
• Qsamtofastq by @ChristinaXu2017 in #283
• update document for qmule by @ChristinaXu2017 in #284
• Qsignature Compare - handle empty vcf files by @holmeso in #285
• add exception message to log file by @ChristinaXu2017 in #286
• update log message for qmule::QSamToFastq by @ChristinaXu2017 in #287
• create new qsv document by @ChristinaXu2017 in #268
• create new qpileup document by @ChristinaXu2017 in #274
• Qprofiler2.doc by @ChristinaXu2017 in #288
• Qsignature - use cutoffs specified in options by @holmeso in #291
• qp2 - use s3 aware reader by @holmeso in #290
• remove class loading by @holmeso in #293
• Update import order in google_check.xml by @holmeso in #292
• qsignature cleanup by @holmeso in #295
• check isPresent before calling get on Optional by @holmeso in #299
• q3tiled_aligner cleanup by @holmeso in #300
• tidy up qmito by @ChristinaXu2017 in #297
• q3indel cleanup by @holmeso in #296
• continue on qmito.doc by @ChristinaXu2017 in #301
• tidy up qcoverage by @ChristinaXu2017 in #294
• fix bug in qpileup view mode by @ChristinaXu2017 in #302
• Q3ta options by @holmeso in #308
• build(all): update htsjdk jar from 2.14.1 to 2.24.1 by @holmeso in #310
• Qpileup.view.bug by @ChristinaXu2017 in #309
• update document on qbasepileup by @ChristinaXu2017 in #311
• fix(q3tiledaligner): remove dependence on GRCh37 by @holmeso in #313
• fix(qsv): incorrect index value was being passed to method by @holmeso in #314
• Qsv q3ta bug fix by @holmeso in #315
• refactor(q3tiled_aligner): allow user to pass in cached ref index map by @holmeso in #316
• feat(qsv): use ref index to determine positions by @holmeso in #319
• update MODE:add header line in remove mode by @ChristinaXu2017 in #320

Full Changelog: 78.43982c9...110.a2ced6c