Pierre Gruet pushed to branch upstream at Debian Med / snpeff
Commits: 11a51516 by Pierre Gruet at 2025-02-16T11:22:10+01:00 New upstream version 5.2.f+dfsg - - - - - 143 changed files: - .classpath - config/snpEff.dbs.config - docs/404.html - docs/about/index.html - docs/download/index.html - docs/examples/index.html - docs/help/index.html - docs/index.html - docs/license/index.html - docs/mkdocs.yml - docs/snpeff/additionalann/index.html - docs/snpeff/build_db/index.html - docs/snpeff/build_db_gff_gtf/index.html - docs/snpeff/build_pdb/index.html - docs/snpeff/build_reg/index.html - docs/snpeff/cansersamples/index.html - docs/snpeff/commandline/index.html - docs/snpeff/commands/index.html - docs/snpeff/faq/index.html - docs/snpeff/human_genomes/index.html - docs/snpeff/inputoutput/index.html - docs/snpeff/integration/index.html - docs/snpeff/introduction/index.html - docs/snpeff/outputsummary/index.html - docs/snpeff/running/index.html - docs/snpeff/troubleshooting/index.html - docs/snpsift/annotate/index.html - + docs/snpsift/annotate_mem/index.html - docs/snpsift/casecontrol/index.html - docs/snpsift/concordance/index.html - docs/snpsift/dbnsfp/index.html - docs/snpsift/extractfields/index.html - docs/snpsift/faq/index.html - docs/snpsift/filter/index.html - docs/snpsift/genesets/index.html - docs/snpsift/gt/index.html - docs/snpsift/gwascatalog/index.html - docs/snpsift/intersect/index.html - docs/snpsift/intervals/index.html - docs/snpsift/intervalsindex/index.html - docs/snpsift/introduction/index.html - docs/snpsift/join/index.html - docs/snpsift/phastcons/index.html - docs/snpsift/private/index.html - docs/snpsift/rminfo/index.html - docs/snpsift/rmrefgen/index.html - docs/snpsift/split/index.html - docs/snpsift/tstv/index.html - docs/snpsift/varianttype/index.html - docs/snpsift/vcf2ped/index.html - docs/snpsift/vcfcheck/index.html - docs/versions.txt - docs/xiangyi_lu_donate/index.html - scripts/1kg.sh → scripts/_OLD/1kg.sh - scripts/annotate_demo.sh → scripts/_OLD/annotate_demo.sh - scripts/annotate_demo_GATK.sh → scripts/_OLD/annotate_demo_GATK.sh - scripts/bedEffOnePerLine.pl → scripts/_OLD/bedEffOnePerLine.pl - scripts/cgShore.pl → scripts/_OLD/cgShore.pl - scripts/cgShore.sh → scripts/_OLD/cgShore.sh - scripts/countColumns.py → scripts/_OLD/countColumns.py - scripts/db.pl → scripts/_OLD/db.pl - scripts/extractSequences.pl → scripts/_OLD/extractSequences.pl - scripts/fasta2tab.pl → scripts/_OLD/fasta2tab.pl - scripts/fastaSample.pl → scripts/_OLD/fastaSample.pl - scripts/fastaSplit.pl → scripts/_OLD/fastaSplit.pl - scripts/fastqSplit.pl → scripts/_OLD/fastqSplit.pl - scripts/filterBy.py → scripts/_OLD/filterBy.py - scripts/gffRemovePhase.pl → scripts/_OLD/gffRemovePhase.pl - scripts/isutf8.py → scripts/_OLD/isutf8.py - scripts/join.pl → scripts/_OLD/join.pl - scripts/joinSnpEff.pl → scripts/_OLD/joinSnpEff.pl - scripts/make_and_commit_docs.sh → scripts/_OLD/make_and_commit_docs.sh - scripts/nextProt_filter.pl → scripts/_OLD/nextProt_filter.pl - scripts/ped2vcf.py → scripts/_OLD/ped2vcf.py - scripts/plot.pl → scripts/_OLD/plot.pl - scripts/plotHistogram.pl → scripts/_OLD/plotHistogram.pl - scripts/plotLabel.pl → scripts/_OLD/plotLabel.pl - scripts/plotMA.pl → scripts/_OLD/plotMA.pl - scripts/plotQQ.pl → scripts/_OLD/plotQQ.pl - scripts/plotQQsubsample.pl → scripts/_OLD/plotQQsubsample.pl - scripts/plotSmoothScatter.pl → scripts/_OLD/plotSmoothScatter.pl - scripts/plotXY.pl → scripts/_OLD/plotXY.pl - scripts/queue.pl → scripts/_OLD/queue.pl - scripts/sam2fastq.pl → scripts/_OLD/sam2fastq.pl - scripts/sample.pl → scripts/_OLD/sample.pl - scripts/snpSift_filter_sample_to_number.pl → scripts/_OLD/snpSift_filter_sample_to_number.pl - scripts/sortLine.py → scripts/_OLD/sortLine.py - scripts/splitChr.pl → scripts/_OLD/splitChr.pl - scripts/statsNum.pl → scripts/_OLD/statsNum.pl - scripts/swapCols.pl → scripts/_OLD/swapCols.pl - scripts/transpose.pl → scripts/_OLD/transpose.pl - scripts/txt2fa.pl → scripts/_OLD/txt2fa.pl - scripts/txt2vcf.py → scripts/_OLD/txt2vcf.py - scripts/uniqCount.pl → scripts/_OLD/uniqCount.pl - scripts/uniqCut.pl → scripts/_OLD/uniqCut.pl - scripts/vcfAnnFirst.py → scripts/_OLD/vcfAnnFirst.py - scripts/vcfBareBones.pl → scripts/_OLD/vcfBareBones.pl - scripts/vcfEffHighest.ORI.py → scripts/_OLD/vcfEffHighest.ORI.py - scripts/vcfEffOnePerLine.pl → scripts/_OLD/vcfEffOnePerLine.pl - scripts/vcfFilterSamples.pl → scripts/_OLD/vcfFilterSamples.pl - scripts/vcfInfoOnePerLine.pl → scripts/_OLD/vcfInfoOnePerLine.pl - scripts/vcfOnlyAlts.pl → scripts/_OLD/vcfOnlyAlts.pl - scripts/vcfReduceGenotypes.pl → scripts/_OLD/vcfReduceGenotypes.pl - scripts/vcfRefCorrect.py → scripts/_OLD/vcfRefCorrect.py - scripts/wigSplit.pl → scripts/_OLD/wigSplit.pl - scripts_build/createBundles.pl → scripts_build/_OLD/createBundles.pl - scripts_build/dbNSFP_analise_filed_counts.pl → scripts_build/_OLD/dbNSFP_analise_filed_counts.pl - scripts_build/ensemblVCF2hgvs.pl → scripts_build/_OLD/ensemblVCF2hgvs.pl - scripts_build/ensembl_gtf_versions.py → scripts_build/_OLD/ensembl_gtf_versions.py - scripts_build/ensembl_protein_transcriptId.sh → scripts_build/_OLD/ensembl_protein_transcriptId.sh - scripts_build/file2GenomeName.pl → scripts_build/_OLD/file2GenomeName.pl - scripts_build/genesTxtColumnNames.sh → scripts_build/_OLD/genesTxtColumnNames.sh - scripts_build/gwascatalog2vcf.pl → scripts_build/_OLD/gwascatalog2vcf.pl - scripts_build/hg19_proteinFasta2NM.pl → scripts_build/_OLD/hg19_proteinFasta2NM.pl - scripts_build/hg19_proteinFastaReplaceName.pl → scripts_build/_OLD/hg19_proteinFastaReplaceName.pl - scripts_build/make_check.pl → scripts_build/_OLD/make_check.pl - scripts_build/mirna2bed.pl → scripts_build/_OLD/mirna2bed.pl - scripts_build/mirna2bed.sh → scripts_build/_OLD/mirna2bed.sh - scripts_build/promoterSequences.sh → scripts_build/_OLD/promoterSequences.sh - scripts_build/proteinFasta2NM.pl → scripts_build/_OLD/proteinFasta2NM.pl - scripts_build/randBedIntervals.pl → scripts_build/_OLD/randBedIntervals.pl - scripts_build/run_epigenome_analysis.sh → scripts_build/_OLD/run_epigenome_analysis.sh - scripts_build/sam2fastq.pl → scripts_build/_OLD/sam2fastq.pl - scripts_build/sift2vcf.pl → scripts_build/_OLD/sift2vcf.pl - scripts_build/sift2vcf.sh → scripts_build/_OLD/sift2vcf.sh - scripts_build/stats_monthly_usage.pl → scripts_build/_OLD/stats_monthly_usage.pl - scripts_build/test.Broad_NS_SYN.sh → scripts_build/_OLD/test.Broad_NS_SYN.sh - scripts_build/dbNSFP_sort.pl → scripts_build/dbNSFP/dbNSFP_sort.pl - scripts_build/dbNSFP_split_by_chr.pl → scripts_build/dbNSFP/dbNSFP_split_by_chr.pl - + scripts_build/dbSnp/GCF_000001405.40_GRCh38.p14_assembly_report.txt - + scripts_build/dbSnp/chr2id.txt - + scripts_build/dbSnp/convert.py - scripts_build/pdbCompoundLines.py → scripts_build/pdb/pdbCompoundLines.py - scripts_build/pdbCompoundLines.sh → scripts_build/pdb/pdbCompoundLines.sh - + scripts_build/snpsift_db/build_snpsift_db.bds - + scripts_build/snpsift_db/download_dbs.sh - − spliceSites/u12_branch.pwm - src/docs/index.md - src/docs/mkdocs.yml - src/docs/snpeff/commandline.md - + src/docs/snpsift/annotate_mem.md - src/main/java/org/snpeff/SnpEff.java - test_04_TestCasesEff.csv The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/11a5151607c8288b300316e4edf9dff1eb7d0571 -- View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/11a5151607c8288b300316e4edf9dff1eb7d0571 You're receiving this email because of your account on salsa.debian.org.
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