├── .gitignore ├── .travis.yml ├── AUTHORS ├── Changelog ├── LICENSE ├── Makefile.am ├── NEWS ├── README.md ├── binary_installer.sh ├── bootstrap ├── configure.ac ├── devel-doc ├── FIXME ├── autotools.README ├── best-practices.txt ├── debug.README ├── dist.README ├── docker.README └── git.README ├── dist ├── LoFreq-0.2.tar.gz ├── LoFreq-0.3.1.tar.gz ├── LoFreq-0.3.2.tar.gz ├── LoFreq-0.3.tar.gz ├── LoFreq-0.4.0.tar.gz ├── lofreq-0.5.0.tar.gz ├── lofreq-v0.1.zip ├── lofreq_star-2.0.0-beta-2-linux-x86-64.tgz ├── lofreq_star-2.0.0-beta-2-macosx.tgz ├── lofreq_star-2.0.0-beta-3-linux-x86-64.tgz ├── lofreq_star-2.0.0-beta-3-macosx.tgz ├── lofreq_star-2.0.0-beta-3.tar.gz ├── lofreq_star-2.0.0-beta-linux-x86-64.tgz ├── lofreq_star-2.0.0-beta-macosx.tgz ├── lofreq_star-2.0.0-linux-x86-64.tgz ├── lofreq_star-2.0.0-macosx.tgz ├── lofreq_star-2.0.0-rc-1.tar.gz ├── lofreq_star-2.0.0.tar.gz ├── lofreq_star-2.1.0.tar.gz ├── lofreq_star-2.1.0_linux-x86-64.tgz ├── lofreq_star-2.1.0_macosx.tgz ├── lofreq_star-2.1.1.tar.gz ├── lofreq_star-2.1.1_linux-x86-64.tgz ├── lofreq_star-2.1.1_macosx.tgz ├── lofreq_star-2.1.2.tar.gz ├── lofreq_star-2.1.2_linux-x86-64.tgz ├── lofreq_star-2.1.2_macosx.tgz ├── lofreq_star-2.1.3.1.tar.gz ├── lofreq_star-2.1.3.1_linux-x86-64.tgz ├── lofreq_star-2.1.3.1_macosx.tgz ├── lofreq_star-2.1.4.tar.gz ├── lofreq_star-2.1.4_linux-x86-64.tgz ├── lofreq_star-2.1.5.tar.gz └── lofreq_star-2.1.5_linux-x86-64.tgz ├── m4 ├── ax_pthread.m4 └── ax_with_htslib.m4 ├── snakemake ├── Snakefile ├── cfg.yaml ├── data │ ├── ref.fa │ ├── regions.bed │ ├── sample1_R1.fastq.gz │ ├── sample1_R2.fastq.gz │ └── sample2.fastq.gz ├── dryrun.sh └── ecoli-cfg.yaml ├── src ├── cdflib90.README ├── cdflib90 │ ├── .gitignore │ ├── Makefile.am │ ├── cdflib.h │ ├── dcdflib.c │ ├── ipmpar.c │ └── readme ├── lofreq │ ├── .gitignore │ ├── Makefile.am │ ├── bam_index.c │ ├── bam_index.c.LICENSE │ ├── bam_index.c.README │ ├── bam_md_ext.c │ ├── bam_md_ext.h │ ├── bedidx.c │ ├── bedidx.c.LICENSE │ ├── binom.c │ ├── binom.h │ ├── defaults.h │ ├── fet.c │ ├── fet.c.LICENSE │ ├── fet.h │ ├── kprobaln_ext.c │ ├── kprobaln_ext.h │ ├── lofreq_alnqual.c │ ├── lofreq_alnqual.h │ ├── lofreq_bamstats.c │ ├── lofreq_bamstats.h │ ├── lofreq_call.c │ ├── lofreq_call.h │ ├── lofreq_checkref.c │ ├── lofreq_checkref.h │ ├── lofreq_filter.c │ ├── lofreq_filter.h │ ├── lofreq_indelqual.c │ ├── lofreq_indelqual.h │ ├── lofreq_index.c │ ├── lofreq_index.h │ ├── lofreq_main.c │ ├── lofreq_uniq.c │ ├── lofreq_uniq.h │ ├── lofreq_vcfset.c │ ├── lofreq_vcfset.h │ ├── lofreq_viterbi.c │ ├── lofreq_viterbi.h │ ├── log.c │ ├── log.h │ ├── multtest.c │ ├── multtest.h │ ├── plp.c │ ├── plp.h │ ├── samutils.c │ ├── samutils.h │ ├── snpcaller.c │ ├── snpcaller.h │ ├── utils.c │ ├── utils.h │ ├── vcf.c │ ├── vcf.h │ ├── viterbi.c │ └── viterbi.h ├── scripts │ ├── Makefile.am │ ├── README │ ├── lofreq2_call_pparallel.py │ ├── lofreq2_local.py │ └── lofreq2_somatic.py ├── tools │ ├── .gitignore │ ├── Makefile.am │ ├── README │ ├── lofreq_star │ │ ├── __init__.py │ │ ├── fdr.py │ │ ├── multiple_testing.py │ │ ├── multiple_testing.py.README │ │ ├── multiple_testing.py.org │ │ └── utils.py │ ├── phased_out │ │ ├── lofreq2_filter.py │ │ ├── lofreq2_vcfset.py │ │ ├── vcf.py │ │ └── vcf.py.README │ ├── scripts │ │ ├── lofreq2_add_fake_gt.py │ │ ├── lofreq2_add_sample.py │ │ ├── lofreq2_analyze_somatic_fn.py │ │ ├── lofreq2_bias.py │ │ ├── lofreq2_cluster.py │ │ ├── lofreq2_indel_ovlp.py │ │ ├── lofreq2_local.py │ │ ├── lofreq2_vcfplot.py │ │ └── mutect_alt_allele_in_normal.py │ ├── setup.py │ ├── setup_conf.py.README │ └── setup_conf.py.in └── uthash │ ├── .gitignore │ ├── LICENSE │ ├── Makefile.am │ └── uthash.h └── tests ├── .gitignore ├── af_tests.sh ├── alnqual.sh.FIXME ├── bamstats.sh.FIXME ├── baq-calls-less-than-nobaq.sh ├── bed.sh ├── bgzf_getline.supp ├── binom_vs_poisson.FIXME ├── bonf_auto_vs_dyn.sh ├── consvar_noqual_filter.sh ├── denv2-pseudoclonal-source-qual.sh ├── denv2-pseudoclonal.sh ├── denv2-simulation.sh ├── denv2-validation.sh ├── diff_opts_same_out.sh.OLD ├── doctest.sh ├── ecoli-clone_incl_parallel.sh ├── ecoli_spikein.sh ├── exome_in_silico.sh.FIXME ├── faidx_fetch_seq.supp ├── fdr.sh ├── filter.sh ├── filter_c.sh ├── filter_only_snvs_or_indels.sh ├── icgc-tcga-dream-indel_chr19.sh ├── icgc-tcga-dream-testproject.sh ├── indel_misc.sh ├── indel_qual.sh ├── indels.sh.FIXME ├── is_quiet.sh.FIXME ├── lewis_known.sh.FIXME ├── lib.sh ├── melanoma.sh.FIXME ├── no_snvs_on_cons_indels.sh.FIXME ├── not-matching-ref.sh ├── parallel.sh ├── pseudomonas_jade.sh.FIXME ├── pylint.rc ├── pylint.sh ├── run_all.sh ├── somatic_CHH966_chr22.sh ├── uniq.sh ├── valgrind_call.sh ├── valgrind_uniq.sh ├── valgrind_vcfset.sh ├── valid_vcf_output.sh ├── vcf_setop.sh └── viterbi.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/.travis.yml -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/AUTHORS -------------------------------------------------------------------------------- /Changelog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/Changelog -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/Makefile.am -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/README.md -------------------------------------------------------------------------------- /binary_installer.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/binary_installer.sh -------------------------------------------------------------------------------- /bootstrap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/bootstrap -------------------------------------------------------------------------------- /configure.ac: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/configure.ac -------------------------------------------------------------------------------- /devel-doc/FIXME: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/devel-doc/FIXME -------------------------------------------------------------------------------- /devel-doc/autotools.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/devel-doc/autotools.README -------------------------------------------------------------------------------- /devel-doc/best-practices.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/devel-doc/best-practices.txt -------------------------------------------------------------------------------- /devel-doc/debug.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/devel-doc/debug.README -------------------------------------------------------------------------------- /devel-doc/dist.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/devel-doc/dist.README -------------------------------------------------------------------------------- /devel-doc/docker.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/devel-doc/docker.README -------------------------------------------------------------------------------- /devel-doc/git.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/devel-doc/git.README -------------------------------------------------------------------------------- /dist/LoFreq-0.2.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/LoFreq-0.2.tar.gz -------------------------------------------------------------------------------- /dist/LoFreq-0.3.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/LoFreq-0.3.1.tar.gz -------------------------------------------------------------------------------- /dist/LoFreq-0.3.2.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/LoFreq-0.3.2.tar.gz -------------------------------------------------------------------------------- /dist/LoFreq-0.3.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/LoFreq-0.3.tar.gz -------------------------------------------------------------------------------- /dist/LoFreq-0.4.0.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/LoFreq-0.4.0.tar.gz -------------------------------------------------------------------------------- /dist/lofreq-0.5.0.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq-0.5.0.tar.gz -------------------------------------------------------------------------------- /dist/lofreq-v0.1.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq-v0.1.zip -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-beta-2-linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-beta-2-linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-beta-2-macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-beta-2-macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-beta-3-linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-beta-3-linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-beta-3-macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-beta-3-macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-beta-3.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-beta-3.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-beta-linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-beta-linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-beta-macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-beta-macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0-rc-1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0-rc-1.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.0.0.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.0.0.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.0.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.0.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.0_linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.0_linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.0_macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.0_macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.1.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.1_linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.1_linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.1_macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.1_macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.2.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.2.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.2_linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.2_linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.2_macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.2_macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.3.1.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.3.1.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.3.1_linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.3.1_linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.3.1_macosx.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.3.1_macosx.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.4.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.4.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.4_linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.4_linux-x86-64.tgz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.5.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.5.tar.gz -------------------------------------------------------------------------------- /dist/lofreq_star-2.1.5_linux-x86-64.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/dist/lofreq_star-2.1.5_linux-x86-64.tgz -------------------------------------------------------------------------------- /m4/ax_pthread.m4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/m4/ax_pthread.m4 -------------------------------------------------------------------------------- /m4/ax_with_htslib.m4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/m4/ax_with_htslib.m4 -------------------------------------------------------------------------------- /snakemake/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/snakemake/Snakefile -------------------------------------------------------------------------------- /snakemake/cfg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/snakemake/cfg.yaml -------------------------------------------------------------------------------- /snakemake/data/ref.fa: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /snakemake/data/regions.bed: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /snakemake/data/sample1_R1.fastq.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /snakemake/data/sample1_R2.fastq.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /snakemake/data/sample2.fastq.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /snakemake/dryrun.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/snakemake/dryrun.sh -------------------------------------------------------------------------------- /snakemake/ecoli-cfg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/snakemake/ecoli-cfg.yaml -------------------------------------------------------------------------------- /src/cdflib90.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/cdflib90.README -------------------------------------------------------------------------------- /src/cdflib90/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/cdflib90/.gitignore -------------------------------------------------------------------------------- /src/cdflib90/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/cdflib90/Makefile.am -------------------------------------------------------------------------------- /src/cdflib90/cdflib.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/cdflib90/cdflib.h -------------------------------------------------------------------------------- /src/cdflib90/dcdflib.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/cdflib90/dcdflib.c -------------------------------------------------------------------------------- /src/cdflib90/ipmpar.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/cdflib90/ipmpar.c -------------------------------------------------------------------------------- /src/cdflib90/readme: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/cdflib90/readme -------------------------------------------------------------------------------- /src/lofreq/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/.gitignore -------------------------------------------------------------------------------- /src/lofreq/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/Makefile.am -------------------------------------------------------------------------------- /src/lofreq/bam_index.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/bam_index.c -------------------------------------------------------------------------------- /src/lofreq/bam_index.c.LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/bam_index.c.LICENSE -------------------------------------------------------------------------------- /src/lofreq/bam_index.c.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/bam_index.c.README -------------------------------------------------------------------------------- /src/lofreq/bam_md_ext.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/bam_md_ext.c -------------------------------------------------------------------------------- /src/lofreq/bam_md_ext.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/bam_md_ext.h -------------------------------------------------------------------------------- /src/lofreq/bedidx.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/bedidx.c -------------------------------------------------------------------------------- /src/lofreq/bedidx.c.LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/bedidx.c.LICENSE -------------------------------------------------------------------------------- /src/lofreq/binom.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/binom.c -------------------------------------------------------------------------------- /src/lofreq/binom.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/binom.h -------------------------------------------------------------------------------- /src/lofreq/defaults.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/defaults.h -------------------------------------------------------------------------------- /src/lofreq/fet.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/fet.c -------------------------------------------------------------------------------- /src/lofreq/fet.c.LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/fet.c.LICENSE -------------------------------------------------------------------------------- /src/lofreq/fet.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/fet.h -------------------------------------------------------------------------------- /src/lofreq/kprobaln_ext.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/kprobaln_ext.c -------------------------------------------------------------------------------- /src/lofreq/kprobaln_ext.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/kprobaln_ext.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_alnqual.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_alnqual.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_alnqual.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_alnqual.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_bamstats.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_bamstats.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_bamstats.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_bamstats.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_call.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_call.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_call.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_call.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_checkref.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_checkref.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_checkref.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_checkref.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_filter.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_filter.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_filter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_filter.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_indelqual.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_indelqual.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_indelqual.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_indelqual.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_index.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_index.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_index.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_index.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_main.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_main.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_uniq.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_uniq.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_uniq.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_uniq.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_vcfset.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_vcfset.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_vcfset.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_vcfset.h -------------------------------------------------------------------------------- /src/lofreq/lofreq_viterbi.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_viterbi.c -------------------------------------------------------------------------------- /src/lofreq/lofreq_viterbi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/lofreq_viterbi.h -------------------------------------------------------------------------------- /src/lofreq/log.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/log.c -------------------------------------------------------------------------------- /src/lofreq/log.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/log.h -------------------------------------------------------------------------------- /src/lofreq/multtest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/multtest.c -------------------------------------------------------------------------------- /src/lofreq/multtest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/multtest.h -------------------------------------------------------------------------------- /src/lofreq/plp.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/plp.c -------------------------------------------------------------------------------- /src/lofreq/plp.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/plp.h -------------------------------------------------------------------------------- /src/lofreq/samutils.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/samutils.c -------------------------------------------------------------------------------- /src/lofreq/samutils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/samutils.h -------------------------------------------------------------------------------- /src/lofreq/snpcaller.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/snpcaller.c -------------------------------------------------------------------------------- /src/lofreq/snpcaller.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/snpcaller.h -------------------------------------------------------------------------------- /src/lofreq/utils.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/utils.c -------------------------------------------------------------------------------- /src/lofreq/utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/utils.h -------------------------------------------------------------------------------- /src/lofreq/vcf.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/vcf.c -------------------------------------------------------------------------------- /src/lofreq/vcf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/vcf.h -------------------------------------------------------------------------------- /src/lofreq/viterbi.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/viterbi.c -------------------------------------------------------------------------------- /src/lofreq/viterbi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/lofreq/viterbi.h -------------------------------------------------------------------------------- /src/scripts/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/scripts/Makefile.am -------------------------------------------------------------------------------- /src/scripts/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/scripts/README -------------------------------------------------------------------------------- /src/scripts/lofreq2_call_pparallel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/scripts/lofreq2_call_pparallel.py -------------------------------------------------------------------------------- /src/scripts/lofreq2_local.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/scripts/lofreq2_local.py -------------------------------------------------------------------------------- /src/scripts/lofreq2_somatic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/scripts/lofreq2_somatic.py -------------------------------------------------------------------------------- /src/tools/.gitignore: -------------------------------------------------------------------------------- 1 | ./build 2 | setup_conf.py 3 | -------------------------------------------------------------------------------- /src/tools/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/Makefile.am -------------------------------------------------------------------------------- /src/tools/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/README -------------------------------------------------------------------------------- /src/tools/lofreq_star/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/lofreq_star/__init__.py -------------------------------------------------------------------------------- /src/tools/lofreq_star/fdr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/lofreq_star/fdr.py -------------------------------------------------------------------------------- /src/tools/lofreq_star/multiple_testing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/lofreq_star/multiple_testing.py -------------------------------------------------------------------------------- /src/tools/lofreq_star/multiple_testing.py.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/lofreq_star/multiple_testing.py.README -------------------------------------------------------------------------------- /src/tools/lofreq_star/multiple_testing.py.org: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/lofreq_star/multiple_testing.py.org -------------------------------------------------------------------------------- /src/tools/lofreq_star/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/lofreq_star/utils.py -------------------------------------------------------------------------------- /src/tools/phased_out/lofreq2_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/phased_out/lofreq2_filter.py -------------------------------------------------------------------------------- /src/tools/phased_out/lofreq2_vcfset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/phased_out/lofreq2_vcfset.py -------------------------------------------------------------------------------- /src/tools/phased_out/vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/phased_out/vcf.py -------------------------------------------------------------------------------- /src/tools/phased_out/vcf.py.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/phased_out/vcf.py.README -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_add_fake_gt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_add_fake_gt.py -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_add_sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_add_sample.py -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_analyze_somatic_fn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_analyze_somatic_fn.py -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_bias.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_bias.py -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_cluster.py -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_indel_ovlp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_indel_ovlp.py -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_local.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_local.py -------------------------------------------------------------------------------- /src/tools/scripts/lofreq2_vcfplot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/lofreq2_vcfplot.py -------------------------------------------------------------------------------- /src/tools/scripts/mutect_alt_allele_in_normal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/scripts/mutect_alt_allele_in_normal.py -------------------------------------------------------------------------------- /src/tools/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/setup.py -------------------------------------------------------------------------------- /src/tools/setup_conf.py.README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/setup_conf.py.README -------------------------------------------------------------------------------- /src/tools/setup_conf.py.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/tools/setup_conf.py.in -------------------------------------------------------------------------------- /src/uthash/.gitignore: -------------------------------------------------------------------------------- 1 | ./uthash-* 2 | 3 | -------------------------------------------------------------------------------- /src/uthash/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/uthash/LICENSE -------------------------------------------------------------------------------- /src/uthash/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/uthash/Makefile.am -------------------------------------------------------------------------------- /src/uthash/uthash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/src/uthash/uthash.h -------------------------------------------------------------------------------- /tests/.gitignore: -------------------------------------------------------------------------------- 1 | data 2 | -------------------------------------------------------------------------------- /tests/af_tests.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/af_tests.sh -------------------------------------------------------------------------------- /tests/alnqual.sh.FIXME: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/alnqual.sh.FIXME -------------------------------------------------------------------------------- /tests/bamstats.sh.FIXME: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/bamstats.sh.FIXME -------------------------------------------------------------------------------- /tests/baq-calls-less-than-nobaq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/baq-calls-less-than-nobaq.sh -------------------------------------------------------------------------------- /tests/bed.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/bed.sh -------------------------------------------------------------------------------- /tests/bgzf_getline.supp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/bgzf_getline.supp -------------------------------------------------------------------------------- /tests/binom_vs_poisson.FIXME: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/binom_vs_poisson.FIXME -------------------------------------------------------------------------------- /tests/bonf_auto_vs_dyn.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/bonf_auto_vs_dyn.sh -------------------------------------------------------------------------------- /tests/consvar_noqual_filter.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/consvar_noqual_filter.sh -------------------------------------------------------------------------------- /tests/denv2-pseudoclonal-source-qual.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/denv2-pseudoclonal-source-qual.sh -------------------------------------------------------------------------------- /tests/denv2-pseudoclonal.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/denv2-pseudoclonal.sh -------------------------------------------------------------------------------- /tests/denv2-simulation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/denv2-simulation.sh -------------------------------------------------------------------------------- /tests/denv2-validation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/denv2-validation.sh -------------------------------------------------------------------------------- /tests/diff_opts_same_out.sh.OLD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/diff_opts_same_out.sh.OLD -------------------------------------------------------------------------------- /tests/doctest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/doctest.sh -------------------------------------------------------------------------------- /tests/ecoli-clone_incl_parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/ecoli-clone_incl_parallel.sh -------------------------------------------------------------------------------- /tests/ecoli_spikein.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/ecoli_spikein.sh -------------------------------------------------------------------------------- /tests/exome_in_silico.sh.FIXME: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/faidx_fetch_seq.supp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/faidx_fetch_seq.supp -------------------------------------------------------------------------------- /tests/fdr.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/fdr.sh -------------------------------------------------------------------------------- /tests/filter.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/filter.sh -------------------------------------------------------------------------------- /tests/filter_c.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/filter_c.sh -------------------------------------------------------------------------------- /tests/filter_only_snvs_or_indels.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/filter_only_snvs_or_indels.sh -------------------------------------------------------------------------------- /tests/icgc-tcga-dream-indel_chr19.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/icgc-tcga-dream-indel_chr19.sh -------------------------------------------------------------------------------- /tests/icgc-tcga-dream-testproject.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/icgc-tcga-dream-testproject.sh -------------------------------------------------------------------------------- /tests/indel_misc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/indel_misc.sh -------------------------------------------------------------------------------- /tests/indel_qual.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/indel_qual.sh -------------------------------------------------------------------------------- /tests/indels.sh.FIXME: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/indels.sh.FIXME -------------------------------------------------------------------------------- /tests/is_quiet.sh.FIXME: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/lewis_known.sh.FIXME: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/lib.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/lib.sh -------------------------------------------------------------------------------- /tests/melanoma.sh.FIXME: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/no_snvs_on_cons_indels.sh.FIXME: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/no_snvs_on_cons_indels.sh.FIXME -------------------------------------------------------------------------------- /tests/not-matching-ref.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/not-matching-ref.sh -------------------------------------------------------------------------------- /tests/parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/parallel.sh -------------------------------------------------------------------------------- /tests/pseudomonas_jade.sh.FIXME: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/pylint.rc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/pylint.rc -------------------------------------------------------------------------------- /tests/pylint.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/pylint.sh -------------------------------------------------------------------------------- /tests/run_all.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/run_all.sh -------------------------------------------------------------------------------- /tests/somatic_CHH966_chr22.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/somatic_CHH966_chr22.sh -------------------------------------------------------------------------------- /tests/uniq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/uniq.sh -------------------------------------------------------------------------------- /tests/valgrind_call.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/valgrind_call.sh -------------------------------------------------------------------------------- /tests/valgrind_uniq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/valgrind_uniq.sh -------------------------------------------------------------------------------- /tests/valgrind_vcfset.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/valgrind_vcfset.sh -------------------------------------------------------------------------------- /tests/valid_vcf_output.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/valid_vcf_output.sh -------------------------------------------------------------------------------- /tests/vcf_setop.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/vcf_setop.sh -------------------------------------------------------------------------------- /tests/viterbi.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/lofreq/HEAD/tests/viterbi.sh --------------------------------------------------------------------------------