Release 1.5.0

Major security bug:

• Forcing log4j transitive dependency (through GKL) to version that doesn't have zero day exploit (#747 and #751)
  See CVE-2021-44228.

Updates to tools in this release:

• AnnotateBamWithUmis
  • Should ignore extra FASTQ records with --sorted (#735)
  • Optionally annotate UMI base qualities (#733)
  • Fix a bug where molecular barcodes be truncated. This only occurs
    with read structures that have either no molecular barcodes or two or more
    molecular barcodes (#742).
  • Add support for multiple input FASTQs (#657)
• PickIlluminaIndices to choose from an existing set of candidates (#641)
• FastqToBam can output UMI qualities (#740)
• FilterSomaticVcf adds the end repair artifact filter (#677)

Updates to APIs in this release:

• Add better error messages for malformed input to Metric classes (#755)
• Log the last record when sorting and writing SAM/BAM (#650)
• Removed the IterableThreadLocal class and use the one in commons (#730)
• Add queryname sorted SamRecord and Template iterators (#516)
• Allow VcfWriter to write to file links, devices, and named pipes (#753)
• Update Intel GKL to 0.8.8 to pull in bug fixes (#676)
• Speed up property access on Cigar case class (#754)
• Skip empty lines at end of sample sheet when parsing sample data (#737)
• Updates the commons dependency to 1.3.0, to include a bug fix (fulcrumgenomics/commons#74)

Thank-you to existing and new contributors:

• Fulcrum Genomics:
  • Tim Fennell (@tfenne)
  • Nils Homer (@nh13)
  • Kari Stromhaug (@kstromhaug)
• Twinstrand Biosciences:
  • Clint Valentine (@clintval)
  • Michael Hipp (@mjhipp)
  • Thomas Smith (@ThomasHSmith)
• Outside contribtors
  • Jordi (@Poshi)

And thank-you to the users!