v0.4.20

add support for Octopus variant caller, handle more VCF/Annovar output formats, fix custom tool support

v0.4.15

Handle VCF data column being called Otherinfo1 instead of Otherinfo

v0.4.14

bump version

v0.4.13

Fix some broken requirements that were pulling in versions with breaking changes. Replace pd.io.common with pd.errors. Add experimental support for using wecall as a variant caller.

v0.4.11

• fix issues when a reference genome without chr prefix was used together with Annovar indices that did have a chr prefix
• update deprecated code
• update documentation

v0.4.9

• add support for MIPGEN's picked_mips.txt file
• support MIPGEN probes with SNPs (probes geneAex1_SNP_a and geneAex1_SNP_b will be merged into a single probe called geneAex1)
• output a more detailed error message when no matching reads were found
• add tests

v0.4.8

• Add support for custom aligners/variant callers
• Change default variant caller to GATK
• Add prefix option for Picard tools
• Fix crash if no variants found
• Add CircleCI for automated testing
• Add automated tests for variant merging, FGFR2/TLK2 tutorials

v0.4.7

• Support running without annotation or with different sets of Annovar indices
• Dockerfile improvements
• Handle variant calls outside target regions
• Add pipeline diagram
• Add test for variant merging

v0.4.6

• fix minor code warnings
• fix dependencies (require UMI-tools <1.0)
• add Dockerfile and update installation instructions

v0.4.5

• improve error message when no reads with matching primers were found
• fix error when use_raw_reads is true and aligner is BWA