SpeedSeq v0.1.2

• Update to SVTyper v0.1.0

SpeedSeq v0.1.0

• Software upgrades to BWA v0.7.10 and FreeBayes 0.9.21
• By default, flag split-reads as supplementary (0x800) rather than secondary (0x100)). This prepares for GRCh38 and alternate contigs.
• SVTyper updates:
  • no longer assumes non-reference genotype. Can be used to naively genotype variants that may be homozygous reference
  • generates empirical histogram of insert sizes
  • examines both sides of INV (inversion) variants
  • better overflow/underflow protection
• Reduced filesize of splitter and discordant BAM files by omitting the superfluous sequence and quality strings

SpeedSeq v0.0.3a

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formatting

SpeedSeq v0.0.3

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