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Squashed #907 and ran format-sources #908

Merged
merged 1 commit into from
Jan 7, 2016
Merged

Squashed #907 and ran format-sources #908

merged 1 commit into from
Jan 7, 2016

Commits on Jan 7, 2016

  1. Fix various minor code issues: 

    * disuse of builtin functions for common reduce operations
* unneceessary toString
* risky/anti-idiomatic Option usage
* Cleaning up TODOs in Vcfutils
* retire VcfStringUtils
* finer exception types in some places
* more explicit Fastq error message in stringent mode
* allow IUPAC codes as isRegularBase alternatives
* Add debug output for Fastq record
    @huitseeker @fnothaft
    huitseeker authored and fnothaft committed Jan 7, 2016
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