Table of Contents - bio-vcf-0.9.5 Documentation
Pages
- LICENSE
-
README
- bio-vcf
- Bio-vcf
- Options
- Performance
- Install
- Command line interface (CLI)
- Special functions
- DbSNP
- Set analysis
- Genotype processing
- Sample counting
- Reorder filter with lambda
- Modify VCF files
- RDF output
- Templates
- Metadata
- Using full VCF header (meta) info
- Statistics
- Other examples
- API
- VCFFile
- Trouble shooting
- MRI supports threading
- Set TMPDIR when running out of space
- Reorder filter on time out
- Reduce thread lines on timeout
- Development
- Debugging
- Could not find rake-10.4.2 in any of the sources
- Tmpdir contains (old) bio-vcf directories
- Project home page
- Cite
- Biogems.info
- Copyright
Classes and Modules
- Bio
- Bio::Template
- BioVcf
- BioVcf::BedFilter
- BioVcf::ConvertStringToValue
- BioVcf::RDF
- BioVcf::Turtle
- BioVcf::VCFfile
- BioVcf::ValueError
- BioVcf::Variant
- BioVcf::VcfAltInfoList
- BioVcf::VcfGenotypeField
- BioVcf::VcfGenotypeFields
- BioVcf::VcfHeader
- BioVcf::VcfHeaderParser
- BioVcf::VcfHeaderParser::RagelKeyValues
- BioVcf::VcfLine
- BioVcf::VcfNucleotideCount4
- BioVcf::VcfRdf
- BioVcf::VcfRecord
- BioVcf::VcfRecordCall
- BioVcf::VcfRecordInfo
- BioVcf::VcfRecordParser
- BioVcf::VcfSample
- BioVcf::VcfSample::Sample
- BioVcf::VcfStatistics
- BioVcf::VcfValue
- PCOWS
- RegressionTest
- RegressionTest::CliExec
Methods
- ::apply_threshold — BioVcf::Variant
- ::compare_files — RegressionTest::CliExec
- ::convert — BioVcf::ConvertStringToValue
- ::debug — BioVcf::VcfHeaderParser::RagelKeyValues
- ::diff — BioVcf::Variant
- ::empty? — BioVcf::VcfValue
- ::empty? — BioVcf::VcfSample
- ::escape_string_literal — BioVcf::RDF
- ::exec — RegressionTest::CliExec
- ::float? — BioVcf::ConvertStringToValue
- ::get_column_names — BioVcf::VcfHeaderParser
- ::get_format — BioVcf::VcfRecordParser
- ::get_info — BioVcf::VcfRecordParser
- ::header — BioVcf::VcfRdf
- ::identifier — BioVcf::Turtle
- ::index — BioVcf::Variant
- ::integer? — BioVcf::ConvertStringToValue
- ::mangle_identifier — BioVcf::Turtle
- ::new — BioVcf::BedFilter
- ::new — PCOWS
- ::new — Bio::Template
- ::new — BioVcf::VCFfile
- ::new — BioVcf::VcfNucleotideCount4
- ::new — BioVcf::VcfAltInfoList
- ::new — BioVcf::VcfGenotypeField
- ::new — BioVcf::VcfGenotypeFields
- ::new — BioVcf::VcfHeader
- ::new — BioVcf::VcfRecordInfo
- ::new — BioVcf::VcfRecord
- ::new — BioVcf::VcfSample::Sample
- ::new — BioVcf::VcfStatistics
- ::parse — BioVcf::VcfLine
- ::parse_field — BioVcf::VcfHeaderParser
- ::quoted_stringify_literal — BioVcf::RDF
- ::record — BioVcf::VcfRdf
- ::relative_diff — BioVcf::Variant
- ::relative_threshold_diff — BioVcf::Variant
- ::run_lexer — BioVcf::VcfHeaderParser::RagelKeyValues
- ::stringify_literal — BioVcf::RDF
- ::stringify_literal — BioVcf::Turtle
- ::threshold_diff — BioVcf::Variant
- ::valid_uri? — BioVcf::RDF
- #[] — BioVcf::VcfNucleotideCount4
- #[] — BioVcf::VcfAltInfoList
- #[] — BioVcf::VcfGenotypeFields
- #[] — BioVcf::VcfRecordInfo
- #[] — BioVcf::VcfSample::Sample
- #[]= — BioVcf::VcfRecordInfo
- #ad — BioVcf::VcfGenotypeField
- #add — BioVcf::VcfHeader
- #add — BioVcf::VcfStatistics
- #add_to_filter_field — BioVcf::VcfRecord
- #alt — BioVcf::VcfRecord
- #amq — BioVcf::VcfGenotypeField
- #bcount — BioVcf::VcfGenotypeField
- #body — Bio::Template
- #bq — BioVcf::VcfGenotypeField
- #cache_method — BioVcf::VcfSample::Sample
- #caching_eval — BioVcf::VcfSample::Sample
- #call_diff — BioVcf::VcfRecordCall
- #call_normal_count — BioVcf::VcfRecordCall
- #call_nuc — BioVcf::VcfRecordCall
- #call_tumor_count — BioVcf::VcfRecordCall
- #call_tumor_relative_count — BioVcf::VcfRecordCall
- #chr — BioVcf::VcfRecord
- #chrom — BioVcf::VcfRecord
- #cleanup — PCOWS
- #cleanup_keep_file — PCOWS
- #cleanup_tmpdir — PCOWS
- #column_names — BioVcf::VcfHeader
- #columns — BioVcf::VcfHeader
- #contains — BioVcf::BedFilter
- #contig — BioVcf::VcfHeader
- #cpu_count — PCOWS
- #dp4 — BioVcf::VcfGenotypeField
- #each — BioVcf::VCFfile
- #each_sample — BioVcf::VcfRecord
- #efilter — BioVcf::VcfSample::Sample
- #empty? — BioVcf::VcfGenotypeField
- #empty? — BioVcf::VcfSample::Sample
- #eval — BioVcf::VcfRecord
- #eval — BioVcf::VcfSample::Sample
- #fetch — BioVcf::VcfGenotypeField
- #fetch_value — BioVcf::VcfGenotypeField
- #fetch_values — BioVcf::VcfSample::Sample
- #fields — BioVcf::VcfRecordInfo
- #filter — BioVcf::VcfHeader
- #filter — BioVcf::VcfRecord
- #find_field — BioVcf::VcfHeader
- #find_fields — BioVcf::VcfHeader
- #first — BioVcf::VcfRecord
- #footer — Bio::Template
- #format — BioVcf::VcfHeader
- #format — BioVcf::VcfRecord
- #gatkcommandline — BioVcf::VcfHeader
- #get_gt — BioVcf::VcfRecordCall
- #gfilter — BioVcf::VcfRecord
- #gti — BioVcf::VcfGenotypeField
- #gti — BioVcf::VcfSample::Sample
- #gti? — BioVcf::VcfGenotypeField
- #gtindex — BioVcf::VcfSample::Sample
- #gts — BioVcf::VcfGenotypeField
- #gts — BioVcf::VcfSample::Sample
- #gts? — BioVcf::VcfGenotypeField
- #header — Bio::Template
- #id — BioVcf::VcfRecord
- #ids — BioVcf::VcfRecord
- #ifilter — BioVcf::VcfSample::Sample
- #ilist — BioVcf::VcfGenotypeField
- #index — BioVcf::VcfRecordCall
- #info — BioVcf::VcfHeader
- #info — BioVcf::VcfRecord
- #max — BioVcf::VcfNucleotideCount4
- #max — BioVcf::VcfAltInfoList
- #meta — BioVcf::VcfHeader
- #method_missing — BioVcf::VcfGenotypeField
- #method_missing — BioVcf::VcfGenotypeFields
- #method_missing — BioVcf::VcfHeader
- #method_missing — BioVcf::VcfRecordInfo
- #method_missing — BioVcf::VcfRecord
- #method_missing — BioVcf::VcfSample::Sample
- #min — BioVcf::VcfNucleotideCount4
- #min — BioVcf::VcfAltInfoList
- #missing_samples? — BioVcf::VcfRecord
- #mktmpfilename — PCOWS
- #multi_threaded — PCOWS
- #normal — BioVcf::VcfRecord
- #num_samples — BioVcf::VcfHeader
- #parse — Bio::Template
- #parseVCFheader — BioVcf::VCFfile
- #pid_or_file_running? — PCOWS
- #pid_running? — PCOWS
- #pl — BioVcf::VcfGenotypeField
- #pos — BioVcf::VcfRecord
- #print — BioVcf::VcfStatistics
- #printable_header_line — BioVcf::VcfHeader
- #process_output — PCOWS
- #process_remaining_output — PCOWS
- #qual — BioVcf::VcfRecord
- #ref — BioVcf::VcfRecord
- #result — Bio::Template
- #sample — BioVcf::VcfRecord
- #sample_by_index — BioVcf::VcfRecord
- #sample_by_name — BioVcf::VcfRecord
- #sample_index — BioVcf::VcfHeader
- #sample_subset_index — BioVcf::VcfHeader
- #samples — BioVcf::VcfHeader
- #samples — BioVcf::VcfRecord
- #samples_index_array — BioVcf::VcfHeader
- #sfilter — BioVcf::VcfSample::Sample
- #single_threaded — PCOWS
- #split_fields — BioVcf::VcfRecordInfo
- #submit_final_worker — PCOWS
- #submit_worker — PCOWS
- #sum — BioVcf::VcfNucleotideCount4
- #sum — BioVcf::VcfAltInfoList
- #tag — BioVcf::VcfHeader
- #to_ary — BioVcf::VcfNucleotideCount4
- #to_ary — BioVcf::VcfAltInfoList
- #to_s — BioVcf::VcfGenotypeField
- #to_s — BioVcf::VcfRecordInfo
- #tumor — BioVcf::VcfRecord
- #valid? — BioVcf::VcfGenotypeField
- #valid? — BioVcf::VcfRecord
- #version — BioVcf::VcfHeader
- #wait_for_worker — PCOWS
- #wait_for_worker_slot — PCOWS
- #wait_for_workers — PCOWS