RatesTools version 0.5.15

• Fixes bug in GATK4 pipeline in which GATK site filters are not applied appropriately

Full Changelog: v0.5.14...v0.5.15

RatesTools version 0.5.14

• Set default number of cpus for RepeatModeler as 2
• Provided handling for non-sensical RepeatModeler cpu requests

Full Changelog: v0.5.13...v0.5.14

RatesTools version 0.5.13

• Fixes bug in repeatMaskRM during RM2bed concatenation
• Retains tbl file of first round of repeat-masking

RatesTools version 0.5.12

• Fixes a bug in RepeatMasker where the initial round of repeat-masking was hard-masked when fed to RepeatModeler and thus these initial repeat annotations were lost.
• Improves temporary file disk usage for GATK site filtration

Full Changelog: v0.5.11...v0.5.12

RatesTools version 0.5.11

Fixes glitch in summarizeDNM that caused crash when no candidate DNM sites were found.

RatesTools version 0.5.10

• Parameters for minimum contig length to retain for analysis

RatesTools version 0.5.9

• Adds handling for selfing parent in calc_denovo_mutation_rate.rb

RatesTools version 0.5.8

Adds support for Conda-based installations

RatesTools version 0.5.7

• Removed unnecessary makefile
• Removed threading parameters and using $task.cpus instead
• Made binaries executable
• Updated documentation

RatesTools version 0.5.6

Bug fixes and minor improvements to region filtration