Changelogs » Amplimap

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- 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


- 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


- 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


- 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


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


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


- updated documentation, add list of supported protocols
  - renamed `tagged_bams_in` to `mapped_bams_in`
  - added check to make sure only one input directory exists
  - added check to confirm that `use_raw_reads` is set when using `unmapped_bams_in` or `mapped_bams_in`
  - add link to cluster log documentation when showing error message
  - internal changes:
  + made input rules conditional on input directory existing, to remove some ambiguity when input files are missing
  + make sure `stats_alignment` files are created even with `mapped_bams_in`
  + added test for multiple input directory check


- improved code documentation
  - improved support for running the Snakefile stand-alone rather than through amplimap
  - fixed naive mapping of untrimmed reads
  - updated tutorials
  - removed some deprecated code
  - added `--latency-wait` parameter
  - added new test cases


- fix version check for newer versions of picard tools
  - add `requirements.txt` file
  - internal changes:
  + add tests for config file reading
  + add test for UMI dedup
  + add/improve code documentation
  + refactor config file reading
  + stop recording versions for individual files
  + catch missing cythonized modules


- renamed output directories to match rule names:
  + `analysis/bam` -> `analysis/bams`
  + `analysis/bam/coverage` -> `analysis/bams/coverages`
  + `analysis/pileup` -> `analysis/pileups`
  + `analysis/pileup` -> `analysis/pileups`
  + `analysis/pileup_snps` -> `analysis/pileups_snps`
  + `analysis/umi_dedup` -> `analysis/bams_umi_dedup`
  - added `general: umi_min_consensus_percentage` setting to specify the minimum fraction of reads in a UMI group that have to agree on the consensus
  - add separate `pileups_snps` rule to only run SNP pileups
  - improved check for missing paths
  - fixed crash if config file was present but empty
  - removed excessive logging in `stats_alignment` and `attach_tags_from_unmapped`
  - improved documentation of config file


- added tutorials
  - added rules to check that tools exist in path (and save their version) before trying to run them
  - added check for valid coordinates in probe design file
  - added check for non-overlapping target regions in targets file
  - added support for space-separated SNPs file
  - added `_fraction` columns to long pileups
  - added config error checks
  - added new tests:
  + run with BWA
  + handle UMIs
  + simulate variants
  - fixed bugs:
  + error when mate names ended in /1 and /2
  + probe information missing from pileup files
  + fixed crash on errors with exon annotation file
  - config changes:
  + added comments to default config to explain each option
  + added `general: use_raw_reads` option (should work with with unmapped bams as well as fastqs)
  + removed `no_probe_data` option (now detected through `use_raw_reads`)
  + moved some options from `general` into `parse_reads`:
  * `trim_primers`
  * `trim_min_length`
  * `quality_trim_threshold`
  * `quality_trim_phred_base`
  + changed defaults for `pileup:validate_probe_targets` and `pileup:filter_softclipped` to false
  + changed default variant caller back to Platypus