Activity for Wolfgang Maier
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Wolfgang Maier committed [cbaec6]
Include cached Galaxy test-data in distribution
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Fix symlinks by specifying relative targets
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Add more tests for variant_annotation module
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fix wrong alleles in variant reports
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fixed by [2482ec]
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Reverse-complement EFF allele when reverting ALT during rebase
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mimodd reheader bug with renaming ref sequences in BAM
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correction to the correction: the real cause of the issue is that the SnpEff effect allele (which SnpEff writes correctly in every case) can get out of sync with the ALT column during rebasing (which may rv-complement ALT alleles, but doesn't know about SnpEff effects fields).
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fix wrong alleles in variant reports
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variant call tool should expose more samtools/bcftools options
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Merge Snap and vcf-filter fixes into stable
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allow unspecified start or stop in vcf-filter region filters
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Fix vcf-filter Galaxy wrapper region filter handling
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First-class sanitize tool
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enable variant filtering based on REF and ALT sequences and on snpEff annotations
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batch-level command line options for snap-batch
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variant filtering mini-language to allow for OR-based filters
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remove snap-batch tool
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Clean up SNAPLib source
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Fix two SNAP compile warnings and snap index crash on modern OSes
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Merge updated info tool docs into stable
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Document info tool enhancements
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Merge v0.2 info tool and wrapper enhancements into stable
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Adjust docs version to match package version exactly
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Include full Galaxy data assets in package install
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Bump package version
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Start work on Galaxy wrapper updates
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Pull in Galaxy toolshed-related assets from wrapper repo
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Support new BED output format of mimodd info
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Improve file info Galaxy tool wrapper
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Replace redundant copy of Galaxy tool_config with symlink
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Titles of datasets created with File Information tool
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fixed by https://github.com/wm75/mimodd_galaxy_wrappers/commit/d78d5783eea5d3cc7ccdb16d6ae3a11864beef2c
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Add BED as fileinfo output format
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MiModD on public Galaxy servers
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prepare for ssl certificate expiration
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could not reproduce, plus updated bundled certificate together with pip/setuptools
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bundled pip is incompatible with python3.8
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resolved by upgrade of the bundled versions of pip and setuptools in changeset [a36bcf]
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Fix for rpy2 3.x series
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addressed by [a4c951], which also restores R warnings output suppression for the 3.x series of rpy2
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Welcome
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Titles of datasets created with File Information tool
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fix remap rv strand bug
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handle freebayes-generated vcfs
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offer mapped reads postprocessing
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make annotate tool robust against very verbose snpEff output
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prepare for ssl certificate expiration
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teach tool wrappers about GALAXY_MEMORY_MB
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sample dropdown select menus
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tool-specific temporary file directories
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internal htslib/samtools/bcftools update
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rethink behaviour of pysamtools.header on empty output
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enable autocompletion of mimodd subcommands in shell
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Support for SNAP v1.0
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keep custom rginfo lines in vcf headers in synchrony with sample names
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keep custom rginfo lines in vcf headers in synchrony with sample names
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clean up code base after 0.1.6.1 pyvcf changes
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new RVD (relative variant density) mode for map tool
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handle uninstall/reinstall
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handle uninstall/reinstall
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FDR filter for delcall
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dealing with ANN format remains to be implemented, but should be part of v0.2
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enable deletion calling for only some of the samples in a BCF file
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scaffold-independent parallelization of variant calling
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add anno_links to vectorbase
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OS X wheels should ship with working copy of bwa as an alternative aligner
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make pysamtools functions return running processes that can be waited for
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convert and split vcf/bcf files
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extend covstats tool
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sample dropdown select menus
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teach tool wrappers about GALAXY_MEMORY_MB
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MiModD on public Galaxy servers
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make annotate tool robust against very verbose snpEff output
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prepare for ssl certificate expiration
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Welcome
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fix covstats tool treatment of positions with zero-coverage in all samples
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python3 -m MiModD.__first_run__ should leave package in more useful state
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This issue is only relevant for conda installs, but in them the default shebang line of the mimodd script: #!/usr/bin/env python3 should get resolved at runtime correctly anyway. It is true that the tool wrapper path will not be set, but it is ok to just not support command line Galaxy integration for conda installs. Conda users should instead configure Galaxy to use their system-installed conda instead of setting up a Galaxy-internal one, then install from the toolshed.
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make VCF region filters work without per-sample info
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addressed by changeset [3051ee]
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keep custom rginfo lines in vcf headers in synchrony with sample names
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handle uninstall/reinstall
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FDR filter for delcall
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clean up code base after 0.1.6.1 pyvcf changes
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enable variant filtering based on REF and ALT sequences and on snpEff annotations
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batch-level command line options for snap-batch
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variant filtering mini-language to allow for OR-based filters
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new RVD (relative variant density) mode for map tool
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replace Galaxy List Installed SnpEff genomes tool
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remove snap-batch tool
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add anno_links to vectorbase
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look into supporting Windows via Docker
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convert and split vcf/bcf files
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varreport functionality outline
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allow unspecified start or stop in vcf-filter region filters
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allow variant calling for subsets of samples
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enable deletion calling for only some of the samples in a BCF file
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explore ways to make bam SQ names override ref names during variant calling
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recognize short snpEff version output
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