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MANIFEST
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bin/add_introns
bin/add_reference_seq
bin/annotate_macs_peaks
bin/annotation_summary
bin/benchmark_recursion
bin/CDS_sequence
bin/coding_gene_count
bin/dump_CDS_sequence
bin/examples/gal_example_parser
bin/examples/gal_example_seq_feature_short
bin/examples/gal_example_seq_features
bin/feature2gff
bin/feature_overlaps
bin/gal_indexer
bin/gal_start_stop
bin/gal_variant_classifier
bin/gene_CDS_footprint
bin/get_overlaping_fetures
bin/get_sequence
bin/gff2gtf
bin/gff3_build_genes
bin/gff3_fix_tabs
bin/gff_tool
bin/gff_tool_gal
bin/gtf2gff3
bin/gvf_validator
bin/macs_genes_with_peaks
bin/protein_genes
bin/protein_sequence
bin/remove_transcripts
bin/sandbox/annovar2gvf
bin/sandbox/bdb_feature_overlaps
bin/sandbox/binary_search
bin/sandbox/build_gff_genes
bin/sandbox/cg2gvf
bin/sandbox/cosmic_file_to_gff3
bin/sandbox/dbm_feature_overlaps
bin/sandbox/dbm_feature_overlaps_bin
bin/sandbox/dbsnp2gvf_flat
bin/sandbox/dbsnp2gvf_xml
bin/sandbox/distance_machine
bin/sandbox/distance_machine_barry
bin/sandbox/distance_machine_disease
bin/sandbox/distance_machine_disease2
bin/sandbox/distance_machine_fast
bin/sandbox/distance_machine_faster
bin/sandbox/distance_machine_hash
bin/sandbox/distance_machine_hash2
bin/sandbox/distance_machine_hash2_disease_new
bin/sandbox/distance_machine_list_maker
bin/sandbox/distance_machine_old
bin/sandbox/distance_machine_omim
bin/sandbox/distance_machine_omim_new
bin/sandbox/distance_machine_omim_newer
bin/sandbox/distance_machine_runner
bin/sandbox/distance_machine_runner_parser
bin/sandbox/distance_tree_rename
bin/sandbox/extract_location_genotype
bin/sandbox/feature_overlaps
bin/sandbox/feature_overlaps_cursor
bin/sandbox/feature_overlaps_dbi
bin/sandbox/feature_overlaps_dbi_bin
bin/sandbox/feature_overlaps_old
bin/sandbox/gal_gvf_HGVS
bin/sandbox/gal_load_db
bin/sandbox/genotype_probability
bin/sandbox/gff2sql
bin/sandbox/gff3_validator
bin/sandbox/gvf2annovar_input
bin/sandbox/gvf_tidy
bin/sandbox/gvf_updater
bin/sandbox/hash_feature_overlaps
bin/sandbox/load_gal_database
bin/sandbox/load_gal_database_bin
bin/sandbox/no_caller
bin/sandbox/omicia_omim2gvf
bin/sandbox/snp2gene
bin/sandbox/snp2gene_bin
bin/sandbox/snp_feature_overlaps
bin/sandbox/spec_01_c_snp_classifier
bin/sandbox/ucsc_gene_table_2_gtf
bin/sandbox/ucsc_genes2gff3
bin/sandbox/ucsc_gtf_converter.pl
bin/sandbox/unique_mapping_probability
bin/sandbox/update_ucsc_gff
bin/sandbox/variant_classifier_abstract
bin/splice_complexity
bin/t/add_reference_seq.t
bin/t/annotation_summary.t
bin/t/build_genes.t
bin/t/data/10Gen_Chinese_SNV_chr22.gvf
bin/t/data/10Gen_Chinese_SNV_partial.gvf
bin/t/data/10Gen_Chinese_SNV_partial.gvf.header
bin/t/data/10Gen_Korean_SNV_chr22.gvf
bin/t/data/1KG_VCF4_1_test.vcf
bin/t/data/augustus_short.gtf
bin/t/data/augustus_short.valid.gff3
bin/t/data/basic_snp.txt
bin/t/data/bed_test_genes.bed
bin/t/data/Canis_familiaris_incl_consequences.gvf
bin/t/data/ccdsGene_hg19_chr22.txt
bin/t/data/celera_short.gff
bin/t/data/celera_short.gff3
bin/t/data/chip_all_intervals.txt
bin/t/data/chr22.fa.index
bin/t/data/clinvar_100_rnd_SNV.vat.gvf
bin/t/data/complete_genomics.csv
bin/t/data/complete_genomics_compact.csv
bin/t/data/cuffdiff_gene_exp.diff
bin/t/data/cufflinks_short.gtf
bin/t/data/cufflinks_short.valid.gff3
bin/t/data/current_release.obo
bin/t/data/Danio.short.gtf
bin/t/data/Danio.short.valid.gff3
bin/t/data/dbsnp_flat.txt
bin/t/data/delimitedline_test.txt
bin/t/data/dmel-4-chromosome-r5.46.fasta
bin/t/data/dmel-4-r5.24.no_gff_version.gff
bin/t/data/dmel-4-r5.24.partial.gff
bin/t/data/dmel-4-r5.27_exon_IDS.txt
bin/t/data/dmel-4-r5.46.genes.gff
bin/t/data/dmel-4-r5.46.genes.partial.gff
bin/t/data/dmel-4-r5.46.gff
bin/t/data/dmel-4-r5.46.no_UTR.gff
bin/t/data/Dmel_genes_4.gff
bin/t/data/ds_ch1.short.xml
bin/t/data/ensemble_01_short.gtf
bin/t/data/ensemble_01_short.valid.gff3
bin/t/data/ensGene_hg19_chr22.txt
bin/t/data/exon_hunter.short.gtf
bin/t/data/exon_hunter.short.valid.gff3
bin/t/data/fasta_ant/directory.index
bin/t/data/fasta_ant/lhum_genome_4.0_short.fasta
bin/t/data/fasta_hg18/chr22_hg18.fasta
bin/t/data/file1.txt
bin/t/data/file2.txt
bin/t/data/gal_feature_test.sqlite
bin/t/data/gencode_short.gtf
bin/t/data/gencode_short.valid.gff3
bin/t/data/gff_tool_map_seqids.txt
bin/t/data/gff_tool_validate.txt
bin/t/data/gvf_pragma_template_hg18.txt
bin/t/data/gvf_pragma_template_hg19.txt
bin/t/data/hapmap_genotypes.txt
bin/t/data/hg18_chr22.fa
bin/t/data/hg19_chr22.fa
bin/t/data/Homo_sapiens.GRCh37.73.chr22.short.gff3.gz
bin/t/data/Homo_sapiens_1005.short.gtf
bin/t/data/Homo_sapiens_1005.short.valid.gff3
bin/t/data/hsap_hg18.short.gtf
bin/t/data/hsap_hg18.short.valid.gff3
bin/t/data/interval_1.gff
bin/t/data/interval_2.gff
bin/t/data/interval_3.gff
bin/t/data/knownGene_hg19_chr22.txt
bin/t/data/korean_indel.gff
bin/t/data/korean_snp.gff
bin/t/data/macs_summits.bed
bin/t/data/map_seqids.gff
bin/t/data/map_seqids.txt
bin/t/data/maq_cns2snp.snp
bin/t/data/multi_fasta.fa
bin/t/data/NA12878.annovar_input_short.exonic_variant_function
bin/t/data/na18507_sanger_indel.gff
bin/t/data/NG_027806.1.gff3
bin/t/data/NM_001033828.1.gff3
bin/t/data/NR_036541.1.gff3
bin/t/data/quake_snp.txt
bin/t/data/refGene_hg19_chr22.txt
bin/t/data/refgene_short.gtf
bin/t/data/refgene_short.valid.gff3
bin/t/data/refseq_chr22.trim.gff3
bin/t/data/remove_ids.txt
bin/t/data/samtools_pileup.txt
bin/t/data/set_ops_01.gff
bin/t/data/set_ops_02.gff
bin/t/data/set_ops_03.gff
bin/t/data/smith_ant_snps.gff
bin/t/data/snv_minimal_chr22.gvf
bin/t/data/soap_indel.gff
bin/t/data/soap_snp.gff
bin/t/data/soap_snp.txt
bin/t/data/solid.txt
bin/t/data/solid_snp.txt
bin/t/data/SRR043167.indel.vcf
bin/t/data/template.gff
bin/t/data/template_sequence_alteration.gff
bin/t/data/test.vcf
bin/t/data/test_blend1.gvf
bin/t/data/test_blend2.gvf
bin/t/data/test_blend3.gvf
bin/t/data/trait_o_matic.gff
bin/t/data/twinscan_chr1.short.gtf
bin/t/data/twinscan_chr1.short.valid.gff3
bin/t/data/unknown_01_short.gtf
bin/t/data/unknown_01_short.valid.gff3
bin/t/data/vegaGene_hg19_chr22.txt
bin/t/data/venter_indel.gff
bin/t/data/venter_snp.gff
bin/t/data/watson_cshl.txt
bin/t/data/wgEncodeGencodeManualV4_hg19_chr22.txt
bin/t/fasta_tool.t
bin/t/fastq_tool.t
bin/t/feature2gff.t
bin/t/gal_add_introns.t
bin/t/gal_CDS_sequence.t
bin/t/gal_coding_gene_count.t
bin/t/gal_dump_CDS_sequence.t
bin/t/gal_example_parser.t
bin/t/gal_example_seq_features.t
bin/t/gal_feature_overlaps.t
bin/t/gal_protein_genes.t
bin/t/gal_protein_sequence.t
bin/t/gal_remove_transcripts.t
bin/t/gal_splice_complexity.t
bin/t/gal_start_stop.t
bin/t/gal_validate_proteins.t
bin/t/gal_variant_classifier.t
bin/t/gff3_validator.t
bin/t/gff_tool.sh
bin/t/gff_tool.t
bin/t/gtf2gff3.t
bin/t/gvf_tool.t.sh
bin/t/gvf_validator.t
bin/t/map_seqids.t
bin/t/merge_data.t
bin/t/sam_inspector.t
bin/t/script_test_template.t
bin/t/ucsc2gff.t
bin/t/ucsc_gtf2gff3.t
bin/transcript_count
bin/ucsc2gff
bin/validate_proteins
Build.PL
CHANGELOG
cleanup.sh
dev/GAL_Indexing_Benchmarks.xlsx
docs/html/GAL/Annotation.pm.html
docs/html/GAL/Base.pm.html
docs/html/GAL/index.html
docs/html/GAL/Index.pm.html
docs/html/GAL/Interval.pm.html
docs/html/GAL/Interval/BitVector.pm.html
docs/html/GAL/Interval/NCL.pm.html
docs/html/GAL/Interval/Span.pm.html
docs/html/GAL/List.pm.html
docs/html/GAL/List/Categorical.pm.html
docs/html/GAL/List/Numeric.pm.html
docs/html/GAL/Manual.pm.html
docs/html/GAL/Parser.pm.html
docs/html/GAL/Parser/23andMe.pm.html
docs/html/GAL/Parser/basic_snp.pm.html
docs/html/GAL/Parser/bed.pm.html
docs/html/GAL/Parser/cgi_allJunctionsBeta.pm.html
docs/html/GAL/Parser/cgi_allSvEventsBeta.pm.html
docs/html/GAL/Parser/cgi_cnvSegmentsDiploidBeta.pm.html
docs/html/GAL/Parser/cgi_compact.pm.html
docs/html/GAL/Parser/cgi_complete.pm.html
docs/html/GAL/Parser/cgi_mobileElementInsertionsBeta.pm.html
docs/html/GAL/Parser/chinese_indel.pm.html
docs/html/GAL/Parser/chinese_snp.pm.html
docs/html/GAL/Parser/dbsnp_flat.pm.html
docs/html/GAL/Parser/evan_snp.pm.html
docs/html/GAL/Parser/gff3.pm.html
docs/html/GAL/Parser/gff3_fast.pm.html
docs/html/GAL/Parser/hapmap_genotypes.pm.html
docs/html/GAL/Parser/hgmd_indel.pm.html
docs/html/GAL/Parser/hgmd_snv.pm.html
docs/html/GAL/Parser/korean_indel.pm.html
docs/html/GAL/Parser/korean_snp.pm.html
docs/html/GAL/Parser/maq_cns2snp.pm.html
docs/html/GAL/Parser/na18507_sanger_indel.pm.html
docs/html/GAL/Parser/ncbi_blast_tab.pm.html
docs/html/GAL/Parser/nhgri_data.pm.html
docs/html/GAL/Parser/nhgri_data2.pm.html
docs/html/GAL/Parser/quake_snp.pm.html
docs/html/GAL/Parser/samtools_pileup.pm.html
docs/html/GAL/Parser/soap_snp.pm.html
docs/html/GAL/Parser/solid_snp.pm.html
docs/html/GAL/Parser/template.pm.html
docs/html/GAL/Parser/template_sequence_alteration.pm.html
docs/html/GAL/Parser/trait_o_matic.pm.html
docs/html/GAL/Parser/ucsc_dbsnp_table.pm.html
docs/html/GAL/Parser/ucsc_gene_table.pm.html
docs/html/GAL/Parser/ucsc_kg_table.pm.html
docs/html/GAL/Parser/vaast_smp.pm.html
docs/html/GAL/Parser/VCFv4_0.pm.html
docs/html/GAL/Parser/venter_indel.pm.html
docs/html/GAL/Parser/venter_snp.pm.html
docs/html/GAL/Parser/wang_xlinked_data.pm.html
docs/html/GAL/Parser/watson_cshl.pm.html
docs/html/GAL/Parser/watson_novel_het.pm.html
docs/html/GAL/Parser/watson_novel_hom.pm.html
docs/html/GAL/podstyle.css
docs/html/GAL/Reader.pm.html
docs/html/GAL/Reader/DelimitedLine.pm.html
docs/html/GAL/Reader/RecordParser.pm.html
docs/html/GAL/Reader/Template.pm.html
docs/html/GAL/Run.pm.html
docs/html/GAL/Schema.pm.html
docs/html/GAL/Schema/Result/Attribute.pm.html
docs/html/GAL/Schema/Result/Feature.pm.html
docs/html/GAL/Schema/Result/Feature/cds.pm.html
docs/html/GAL/Schema/Result/Feature/exon.pm.html
docs/html/GAL/Schema/Result/Feature/five_prime_utr.pm.html
docs/html/GAL/Schema/Result/Feature/gene.pm.html
docs/html/GAL/Schema/Result/Feature/intron.pm.html
docs/html/GAL/Schema/Result/Feature/mrna.pm.html
docs/html/GAL/Schema/Result/Feature/protein.pm.html
docs/html/GAL/Schema/Result/Feature/sequence_alteration.pm.html
docs/html/GAL/Schema/Result/Feature/sequence_feature.pm.html
docs/html/GAL/Schema/Result/Feature/template.pm.html
docs/html/GAL/Schema/Result/Feature/three_prime_utr.pm.html
docs/html/GAL/Schema/Result/Feature/transcript.pm.html
docs/html/GAL/Schema/Result/Relationship.pm.html
docs/html/GAL/Schema/ResultSet/Feature.pm.html
docs/html/GAL/SchemaAnnotation.pm.html
docs/html/GAL/src/Annotation.pm
docs/html/GAL/src/Base.pm
docs/html/GAL/src/Index.pm
docs/html/GAL/src/Interval.pm
docs/html/GAL/src/Interval/BitVector.pm
docs/html/GAL/src/Interval/NCL.pm
docs/html/GAL/src/Interval/Span.pm
docs/html/GAL/src/List.pm
docs/html/GAL/src/List/Categorical.pm
docs/html/GAL/src/List/Numeric.pm
docs/html/GAL/src/Manual.pm
docs/html/GAL/src/Parser.pm
docs/html/GAL/src/Parser/23andMe.pm
docs/html/GAL/src/Parser/basic_snp.pm
docs/html/GAL/src/Parser/bed.pm
docs/html/GAL/src/Parser/cgi_allJunctionsBeta.pm
docs/html/GAL/src/Parser/cgi_allSvEventsBeta.pm
docs/html/GAL/src/Parser/cgi_cnvSegmentsDiploidBeta.pm
docs/html/GAL/src/Parser/cgi_compact.pm
docs/html/GAL/src/Parser/cgi_complete.pm
docs/html/GAL/src/Parser/cgi_mobileElementInsertionsBeta.pm
docs/html/GAL/src/Parser/chinese_indel.pm
docs/html/GAL/src/Parser/chinese_snp.pm
docs/html/GAL/src/Parser/dbsnp_flat.pm
docs/html/GAL/src/Parser/evan_snp.pm
docs/html/GAL/src/Parser/gff3.pm
docs/html/GAL/src/Parser/gff3_fast.pm
docs/html/GAL/src/Parser/hapmap_genotypes.pm
docs/html/GAL/src/Parser/hgmd_indel.pm
docs/html/GAL/src/Parser/hgmd_snv.pm
docs/html/GAL/src/Parser/korean_indel.pm
docs/html/GAL/src/Parser/korean_snp.pm
docs/html/GAL/src/Parser/maq_cns2snp.pm
docs/html/GAL/src/Parser/na18507_sanger_indel.pm
docs/html/GAL/src/Parser/ncbi_blast_tab.pm
docs/html/GAL/src/Parser/nhgri_data.pm
docs/html/GAL/src/Parser/nhgri_data2.pm
docs/html/GAL/src/Parser/quake_snp.pm
docs/html/GAL/src/Parser/samtools_pileup.pm
docs/html/GAL/src/Parser/soap_snp.pm
docs/html/GAL/src/Parser/solid_snp.pm
docs/html/GAL/src/Parser/template.pm
docs/html/GAL/src/Parser/template_sequence_alteration.pm
docs/html/GAL/src/Parser/trait_o_matic.pm
docs/html/GAL/src/Parser/ucsc_dbsnp_table.pm
docs/html/GAL/src/Parser/ucsc_gene_table.pm
docs/html/GAL/src/Parser/ucsc_kg_table.pm
docs/html/GAL/src/Parser/vaast_smp.pm
docs/html/GAL/src/Parser/VCFv4_0.pm
docs/html/GAL/src/Parser/venter_indel.pm
docs/html/GAL/src/Parser/venter_snp.pm
docs/html/GAL/src/Parser/wang_xlinked_data.pm
docs/html/GAL/src/Parser/watson_cshl.pm
docs/html/GAL/src/Parser/watson_novel_het.pm
docs/html/GAL/src/Parser/watson_novel_hom.pm
docs/html/GAL/src/Reader.pm
docs/html/GAL/src/Reader/DelimitedLine.pm
docs/html/GAL/src/Reader/RecordParser.pm
docs/html/GAL/src/Reader/Template.pm
docs/html/GAL/src/Run.pm
docs/html/GAL/src/Schema.pm
docs/html/GAL/src/Schema/Result/Attribute.pm
docs/html/GAL/src/Schema/Result/Feature.pm
docs/html/GAL/src/Schema/Result/Feature/cds.pm
docs/html/GAL/src/Schema/Result/Feature/exon.pm
docs/html/GAL/src/Schema/Result/Feature/five_prime_utr.pm
docs/html/GAL/src/Schema/Result/Feature/gene.pm
docs/html/GAL/src/Schema/Result/Feature/intron.pm
docs/html/GAL/src/Schema/Result/Feature/mrna.pm
docs/html/GAL/src/Schema/Result/Feature/protein.pm
docs/html/GAL/src/Schema/Result/Feature/sequence_alteration.pm
docs/html/GAL/src/Schema/Result/Feature/sequence_feature.pm
docs/html/GAL/src/Schema/Result/Feature/template.pm
docs/html/GAL/src/Schema/Result/Feature/three_prime_utr.pm
docs/html/GAL/src/Schema/Result/Feature/transcript.pm
docs/html/GAL/src/Schema/Result/Relationship.pm
docs/html/GAL/src/Schema/ResultSet/Feature.pm
docs/html/GAL/src/SchemaAnnotation.pm
docs/html/GAL/src/Storage.pm
docs/html/GAL/src/Storage/mysql.pm
docs/html/GAL/src/Storage/RAM.pm
docs/html/GAL/src/Storage/SQLite.pm
docs/html/GAL/src/t/devel_scripts/annotation_basic.pl
docs/html/GAL/src/t/devel_scripts/annotation_existing.pl
docs/html/GAL/src/t/devel_scripts/annotation_load_file.pl
docs/html/GAL/src/t/devel_scripts/parser_1000_genomes_genotypes.pl
docs/html/GAL/src/t/devel_scripts/parser_complete_genomics.pl
docs/html/GAL/src/t/devel_scripts/parser_dbsnp_flat.pl
docs/html/GAL/src/t/devel_scripts/parser_illumina_indel.pl
docs/html/GAL/src/t/devel_scripts/parser_na18507_indel.pl
docs/html/GAL/src/t/devel_scripts/parser_quake.pl
docs/html/GAL/src/t/devel_scripts/parser_samtools_pileup.pl
docs/html/GAL/src/t/devel_scripts/parser_smith_ant_snps.pl
docs/html/GAL/src/t/devel_scripts/parser_soap_indel.pl
docs/html/GAL/src/t/devel_scripts/parser_soap_snp.pl
docs/html/GAL/src/t/devel_scripts/parser_trait_o_matic.pl
docs/html/GAL/src/t/devel_scripts/parser_venter_indel.pl
docs/html/GAL/src/t/devel_scripts/schema_cursor.pl
docs/html/GAL/src/t/devel_scripts/schema_dbi.pl
docs/html/GAL/src/t/devel_scripts/schema_hash.pl
docs/html/GAL/src/t/devel_scripts/schema_mysql.pl
docs/html/GAL/src/t/devel_scripts/schema_object.pl
docs/html/GAL/src/t/devel_scripts/storage_mysql.pl
docs/html/GAL/Storage.pm.html
docs/html/GAL/Storage/mysql.pm.html
docs/html/GAL/Storage/RAM.pm.html
docs/html/GAL/Storage/SQLite.pm.html
docs/html/GAL/t/devel_scripts/annotation_basic.pl.html
docs/html/GAL/t/devel_scripts/annotation_existing.pl.html
docs/html/GAL/t/devel_scripts/annotation_load_file.pl.html
docs/html/GAL/t/devel_scripts/parser_1000_genomes_genotypes.pl.html
docs/html/GAL/t/devel_scripts/parser_complete_genomics.pl.html
docs/html/GAL/t/devel_scripts/parser_dbsnp_flat.pl.html
docs/html/GAL/t/devel_scripts/parser_illumina_indel.pl.html
docs/html/GAL/t/devel_scripts/parser_na18507_indel.pl.html
docs/html/GAL/t/devel_scripts/parser_quake.pl.html
docs/html/GAL/t/devel_scripts/parser_samtools_pileup.pl.html
docs/html/GAL/t/devel_scripts/parser_smith_ant_snps.pl.html
docs/html/GAL/t/devel_scripts/parser_soap_indel.pl.html
docs/html/GAL/t/devel_scripts/parser_soap_snp.pl.html
docs/html/GAL/t/devel_scripts/parser_trait_o_matic.pl.html
docs/html/GAL/t/devel_scripts/parser_venter_indel.pl.html
docs/html/GAL/t/devel_scripts/schema_cursor.pl.html
docs/html/GAL/t/devel_scripts/schema_dbi.pl.html
docs/html/GAL/t/devel_scripts/schema_hash.pl.html
docs/html/GAL/t/devel_scripts/schema_mysql.pl.html
docs/html/GAL/t/devel_scripts/schema_object.pl.html
docs/html/GAL/t/devel_scripts/storage_mysql.pl.html
docs/html/GAL/up.gif
docs/html/make_docs.sh
gal-image.jpg
INSTALL
lib/GAL/Annotation.pm
lib/GAL/Base.pm
lib/GAL/List.pm
lib/GAL/List/Categorical.pm
lib/GAL/List/Numeric.pm
lib/GAL/Manual.pm
lib/GAL/Parser.pm
lib/GAL/Parser/23andMe.pm
lib/GAL/Parser/annovar_exonic.pm
lib/GAL/Parser/annovar_variant.pm
lib/GAL/Parser/basic_snp.pm
lib/GAL/Parser/bed.pm
lib/GAL/Parser/blastn_hittable_parser.pm
lib/GAL/Parser/cgi_allJunctionsBeta.pm
lib/GAL/Parser/cgi_allSvEventsBeta.pm
lib/GAL/Parser/cgi_cnvSegmentsDiploidBeta.pm
lib/GAL/Parser/cgi_compact.pm
lib/GAL/Parser/cgi_complete.pm
lib/GAL/Parser/cgi_mobileElementInsertionsBeta.pm
lib/GAL/Parser/chinese_indel.pm
lib/GAL/Parser/chinese_snp.pm
lib/GAL/Parser/cuffdiff_gene_exp.pm
lib/GAL/Parser/dbsnp_flat.pm
lib/GAL/Parser/evan_snp.pm
lib/GAL/Parser/gff3.pm
lib/GAL/Parser/gff3_fast.pm
lib/GAL/Parser/hapmap_genotypes.pm
lib/GAL/Parser/hgmd_indel.pm
lib/GAL/Parser/hgmd_snv.pm
lib/GAL/Parser/korean_indel.pm
lib/GAL/Parser/korean_snp.pm
lib/GAL/Parser/macs_summits.pm
lib/GAL/Parser/maq_cns2snp.pm
lib/GAL/Parser/na18507_sanger_indel.pm
lib/GAL/Parser/ncbi_blast_tab.pm
lib/GAL/Parser/nhgri_data.pm
lib/GAL/Parser/nhgri_data2.pm
lib/GAL/Parser/quake_snp.pm
lib/GAL/Parser/samtools_pileup.pm
lib/GAL/Parser/seattleseq.pm
lib/GAL/Parser/snpeff.pm
lib/GAL/Parser/soap_snp.pm
lib/GAL/Parser/solid_snp.pm
lib/GAL/Parser/template.pm
lib/GAL/Parser/template_sequence_alteration.pm
lib/GAL/Parser/trait_o_matic.pm
lib/GAL/Parser/ucsc_dbsnp_table.pm
lib/GAL/Parser/ucsc_gene_table.pm
lib/GAL/Parser/ucsc_kg_table.pm
lib/GAL/Parser/vaast_smp.pm
lib/GAL/Parser/vat_snyder.pm
lib/GAL/Parser/VCFv4_0.pm
lib/GAL/Parser/VCFv4_1.pm
lib/GAL/Parser/venter_indel.pm
lib/GAL/Parser/venter_snp.pm
lib/GAL/Parser/vep.pm
lib/GAL/Parser/wang_xlinked_data.pm
lib/GAL/Parser/watson_cshl.pm
lib/GAL/Parser/watson_novel_het.pm
lib/GAL/Parser/watson_novel_hom.pm
lib/GAL/Reader.pm
lib/GAL/Reader/DelimitedLine.pm
lib/GAL/Reader/RecordParser.pm
lib/GAL/Reader/Template.pm
lib/GAL/Run.pm
lib/GAL/Schema.pm
lib/GAL/Schema/Result/Attribute.pm
lib/GAL/Schema/Result/Feature.pm
lib/GAL/Schema/Result/Feature/cds.pm
lib/GAL/Schema/Result/Feature/exon.pm
lib/GAL/Schema/Result/Feature/five_prime_utr.pm
lib/GAL/Schema/Result/Feature/gene.pm
lib/GAL/Schema/Result/Feature/intron.pm
lib/GAL/Schema/Result/Feature/mrna.pm
lib/GAL/Schema/Result/Feature/protein.pm
lib/GAL/Schema/Result/Feature/sequence_alteration.pm
lib/GAL/Schema/Result/Feature/sequence_feature.pm
lib/GAL/Schema/Result/Feature/snorna_gene.pm
lib/GAL/Schema/Result/Feature/snrna_gene.pm
lib/GAL/Schema/Result/Feature/template.pm
lib/GAL/Schema/Result/Feature/three_prime_utr.pm
lib/GAL/Schema/Result/Feature/transcript.pm
lib/GAL/Schema/Result/Relationship.pm
lib/GAL/Schema/ResultSet/Feature.pm
lib/GAL/SchemaAnnotation.pm
lib/GAL/Storage.pm
lib/GAL/Storage/mysql.pm
lib/GAL/Storage/RAM.pm
lib/GAL/Storage/SQLite.pm
lib/GAL/t/001_annotation.t
lib/GAL/t/001_base.t
lib/GAL/t/001_pod_coverage.t
lib/GAL/t/001_test_template.t
lib/GAL/t/200_parser.t
lib/GAL/t/200_parser_basic_snp.t
lib/GAL/t/200_parser_bed.t
lib/GAL/t/200_parser_complete_genomics.t
lib/GAL/t/200_parser_complete_genomics_new.t
lib/GAL/t/200_parser_cosmic.t
lib/GAL/t/200_parser_cuffdiff_gene_exp.t
lib/GAL/t/200_parser_dbsnp_flat.t
lib/GAL/t/200_parser_gff3.t
lib/GAL/t/200_parser_hapmap_genotypes.t
lib/GAL/t/200_parser_korean_indel.t
lib/GAL/t/200_parser_korean_snp.t
lib/GAL/t/200_parser_macs_summits.t
lib/GAL/t/200_parser_maq_cns2snp.t
lib/GAL/t/200_parser_na18507_sanger_indel.t
lib/GAL/t/200_parser_quake_snp.t
lib/GAL/t/200_parser_samtools_pileup.t
lib/GAL/t/200_parser_snpeff.t
lib/GAL/t/200_parser_soap_snp.t
lib/GAL/t/200_parser_solid_snp.t
lib/GAL/t/200_parser_template.t
lib/GAL/t/200_parser_template_sequence_alteration.t
lib/GAL/t/200_parser_trait_o_matic.t
lib/GAL/t/200_parser_vcfv4_0.t
lib/GAL/t/200_parser_vcfv4_1.t
lib/GAL/t/200_parser_venter_indel.t
lib/GAL/t/200_parser_venter_snp.t
lib/GAL/t/200_parser_watson_cshl.t
lib/GAL/t/300_reader.t
lib/GAL/t/300_reader_delimitedline.t
lib/GAL/t/300_reader_recordparser.t
lib/GAL/t/300_reader_template.t
lib/GAL/t/400_storage.t
lib/GAL/t/400_storage_mysql.t
lib/GAL/t/400_storage_sqlite.t
lib/GAL/t/500_schema.t
lib/GAL/t/500_schema_result_attribute.t
lib/GAL/t/500_schema_result_feature.t
lib/GAL/t/500_schema_result_feature_cds.t
lib/GAL/t/500_schema_result_feature_exon.t
lib/GAL/t/500_schema_result_feature_five_prime_utr.t
lib/GAL/t/500_schema_result_feature_gene.t
lib/GAL/t/500_schema_result_feature_intron.t
lib/GAL/t/500_schema_result_feature_mrna.t
lib/GAL/t/500_schema_result_feature_mrna_BIG.t
lib/GAL/t/500_schema_result_feature_protein.t
lib/GAL/t/500_schema_result_feature_sequence_alteration.t
lib/GAL/t/500_schema_result_feature_sequence_feature.t
lib/GAL/t/500_schema_result_feature_template.t
lib/GAL/t/500_schema_result_feature_three_prime_utr.t
lib/GAL/t/500_schema_result_feature_transcript.t
lib/GAL/t/500_schema_result_realtionship.t
lib/GAL/t/600_list.t
lib/GAL/t/600_list_categorical.t
lib/GAL/t/600_list_numeric.t
lib/GAL/t/700_writer.t
lib/GAL/t/700_writer_gff3.t
lib/GAL/t/data/10Gen_Chinese_SNV_chr22.gvf
lib/GAL/t/data/10Gen_Chinese_SNV_partial.gvf
lib/GAL/t/data/10Gen_Chinese_SNV_partial.gvf.header
lib/GAL/t/data/10Gen_Korean_SNV_chr22.gvf
lib/GAL/t/data/1KG_VCF4_1_test.vcf
lib/GAL/t/data/augustus_short.gtf
lib/GAL/t/data/augustus_short.valid.gff3
lib/GAL/t/data/basic_snp.txt
lib/GAL/t/data/bed_test_genes.bed
lib/GAL/t/data/Canis_familiaris_incl_consequences.gvf
lib/GAL/t/data/ccdsGene_hg19_chr22.txt
lib/GAL/t/data/celera_short.gff
lib/GAL/t/data/celera_short.gff3
lib/GAL/t/data/chip_all_intervals.txt
lib/GAL/t/data/chr22.fa.index
lib/GAL/t/data/clinvar_100_rnd_SNV.vat.gvf
lib/GAL/t/data/complete_genomics.csv
lib/GAL/t/data/complete_genomics_compact.csv
lib/GAL/t/data/cuffdiff_gene_exp.diff
lib/GAL/t/data/cufflinks_short.gtf
lib/GAL/t/data/cufflinks_short.valid.gff3
lib/GAL/t/data/current_release.obo
lib/GAL/t/data/Danio.short.gtf
lib/GAL/t/data/Danio.short.valid.gff3
lib/GAL/t/data/dbsnp_flat.txt
lib/GAL/t/data/delimitedline_test.txt
lib/GAL/t/data/dmel-4-chromosome-r5.46.fasta
lib/GAL/t/data/dmel-4-r5.24.no_gff_version.gff
lib/GAL/t/data/dmel-4-r5.24.partial.gff
lib/GAL/t/data/dmel-4-r5.27_exon_IDS.txt
lib/GAL/t/data/dmel-4-r5.46.genes.gff
lib/GAL/t/data/dmel-4-r5.46.genes.partial.gff
lib/GAL/t/data/dmel-4-r5.46.gff
lib/GAL/t/data/dmel-4-r5.46.no_UTR.gff
lib/GAL/t/data/Dmel_genes_4.gff
lib/GAL/t/data/ds_ch1.short.xml
lib/GAL/t/data/ensemble_01_short.gtf
lib/GAL/t/data/ensemble_01_short.valid.gff3
lib/GAL/t/data/ensGene_hg19_chr22.txt
lib/GAL/t/data/exon_hunter.short.gtf
lib/GAL/t/data/exon_hunter.short.valid.gff3
lib/GAL/t/data/fasta_ant/directory.index
lib/GAL/t/data/fasta_ant/lhum_genome_4.0_short.fasta
lib/GAL/t/data/fasta_hg18/chr22_hg18.fasta
lib/GAL/t/data/file1.txt
lib/GAL/t/data/file2.txt
lib/GAL/t/data/gal_feature_test.sqlite
lib/GAL/t/data/gencode_short.gtf
lib/GAL/t/data/gencode_short.valid.gff3
lib/GAL/t/data/gff_tool_map_seqids.txt
lib/GAL/t/data/gff_tool_validate.txt
lib/GAL/t/data/gvf_pragma_template_hg18.txt
lib/GAL/t/data/gvf_pragma_template_hg19.txt
lib/GAL/t/data/hapmap_genotypes.txt
lib/GAL/t/data/hg18_chr22.fa
lib/GAL/t/data/hg19_chr22.fa
lib/GAL/t/data/Homo_sapiens.GRCh37.73.chr22.short.gff3.gz
lib/GAL/t/data/Homo_sapiens_1005.short.gtf
lib/GAL/t/data/Homo_sapiens_1005.short.valid.gff3
lib/GAL/t/data/hsap_hg18.short.gtf
lib/GAL/t/data/hsap_hg18.short.valid.gff3
lib/GAL/t/data/interval_1.gff
lib/GAL/t/data/interval_2.gff
lib/GAL/t/data/interval_3.gff
lib/GAL/t/data/knownGene_hg19_chr22.txt
lib/GAL/t/data/korean_indel.gff
lib/GAL/t/data/korean_snp.gff
lib/GAL/t/data/macs_summits.bed
lib/GAL/t/data/map_seqids.gff
lib/GAL/t/data/map_seqids.txt
lib/GAL/t/data/maq_cns2snp.snp
lib/GAL/t/data/multi_fasta.fa
lib/GAL/t/data/NA12878.annovar_input_short.exonic_variant_function
lib/GAL/t/data/na18507_sanger_indel.gff
lib/GAL/t/data/NG_027806.1.gff3
lib/GAL/t/data/NM_001033828.1.gff3
lib/GAL/t/data/NR_036541.1.gff3
lib/GAL/t/data/quake_snp.txt
lib/GAL/t/data/refGene_hg19_chr22.txt
lib/GAL/t/data/refgene_short.gtf
lib/GAL/t/data/refgene_short.valid.gff3
lib/GAL/t/data/refseq_chr22.trim.gff3
lib/GAL/t/data/remove_ids.txt
lib/GAL/t/data/samtools_pileup.txt
lib/GAL/t/data/set_ops_01.gff
lib/GAL/t/data/set_ops_02.gff
lib/GAL/t/data/set_ops_03.gff
lib/GAL/t/data/smith_ant_snps.gff
lib/GAL/t/data/snv_minimal_chr22.gvf
lib/GAL/t/data/soap_indel.gff
lib/GAL/t/data/soap_snp.gff
lib/GAL/t/data/soap_snp.txt
lib/GAL/t/data/solid.txt
lib/GAL/t/data/solid_snp.txt
lib/GAL/t/data/SRR043167.indel.vcf
lib/GAL/t/data/template.gff
lib/GAL/t/data/template_sequence_alteration.gff
lib/GAL/t/data/test.vcf
lib/GAL/t/data/test_blend1.gvf
lib/GAL/t/data/test_blend2.gvf
lib/GAL/t/data/test_blend3.gvf
lib/GAL/t/data/trait_o_matic.gff
lib/GAL/t/data/twinscan_chr1.short.gtf
lib/GAL/t/data/twinscan_chr1.short.valid.gff3
lib/GAL/t/data/unknown_01_short.gtf
lib/GAL/t/data/unknown_01_short.valid.gff3
lib/GAL/t/data/vegaGene_hg19_chr22.txt
lib/GAL/t/data/venter_indel.gff
lib/GAL/t/data/venter_snp.gff
lib/GAL/t/data/watson_cshl.txt
lib/GAL/t/data/wgEncodeGencodeManualV4_hg19_chr22.txt
lib/GAL/t/devel_scripts/annotation_basic.pl
lib/GAL/t/devel_scripts/annotation_existing.pl
lib/GAL/t/devel_scripts/annotation_load_file.pl
lib/GAL/t/devel_scripts/parser_1000_genomes_genotypes.pl
lib/GAL/t/devel_scripts/parser_annovar_exonic.pl
lib/GAL/t/devel_scripts/parser_complete_genomics.pl
lib/GAL/t/devel_scripts/parser_dbsnp_flat.pl
lib/GAL/t/devel_scripts/parser_illumina_indel.pl
lib/GAL/t/devel_scripts/parser_na18507_indel.pl
lib/GAL/t/devel_scripts/parser_quake.pl
lib/GAL/t/devel_scripts/parser_samtools_pileup.pl
lib/GAL/t/devel_scripts/parser_smith_ant_snps.pl
lib/GAL/t/devel_scripts/parser_soap_indel.pl
lib/GAL/t/devel_scripts/parser_soap_snp.pl
lib/GAL/t/devel_scripts/parser_trait_o_matic.pl
lib/GAL/t/devel_scripts/parser_venter_indel.pl
lib/GAL/t/devel_scripts/schema_cursor.pl
lib/GAL/t/devel_scripts/schema_dbi.pl
lib/GAL/t/devel_scripts/schema_hash.pl
lib/GAL/t/devel_scripts/schema_mysql.pl
lib/GAL/t/devel_scripts/schema_object.pl
lib/GAL/t/devel_scripts/storage_mysql.pl
lib/GAL/Template.pmx
lib/GAL/templates/gff_tool_gvf_example.tt
lib/GAL/templates/gff_tool_gvf_example2.tt
lib/GAL/templates/soba/HOLD/soba_counts.tt
lib/GAL/templates/soba/HOLD/soba_lengths.tt
lib/GAL/templates/soba/HOLD/test.tt
lib/GAL/templates/soba/HOLD/test2.tt
lib/GAL/templates/soba/soba_custom_template_text.tt
lib/GAL/templates/soba/soba_length_fd.tt
lib/GAL/templates/soba/soba_report_attributes_html.tt
lib/GAL/templates/soba/soba_report_attributes_text.tt
lib/GAL/templates/soba/soba_table_html.tt
lib/GAL/templates/soba/soba_table_html_page.tt
lib/GAL/templates/soba/soba_table_tab.tt
lib/GAL/templates/soba/soba_table_text.tt
lib/GAL/Writer.pm
lib/GAL/Writer/GFF3.pm
LICENSE
MANIFEST This list of files
META.json
META.yml
README
README.md
t/data/10Gen_Chinese_SNV_chr22.gvf
t/data/10Gen_Chinese_SNV_partial.gvf
t/data/10Gen_Chinese_SNV_partial.gvf.header
t/data/10Gen_Korean_SNV_chr22.gvf
t/data/1KG_VCF4_1_test.vcf
t/data/augustus_short.gtf
t/data/augustus_short.valid.gff3
t/data/basic_snp.txt
t/data/bed_test_genes.bed
t/data/Canis_familiaris_incl_consequences.gvf
t/data/ccdsGene_hg19_chr22.txt
t/data/celera_short.gff
t/data/celera_short.gff3
t/data/chip_all_intervals.txt
t/data/chr22.fa.index
t/data/clinvar_100_rnd_SNV.vat.gvf
t/data/complete_genomics.csv
t/data/complete_genomics_compact.csv
t/data/cuffdiff_gene_exp.diff
t/data/cufflinks_short.gtf
t/data/cufflinks_short.valid.gff3
t/data/current_release.obo
t/data/Danio.short.gtf
t/data/Danio.short.valid.gff3
t/data/dbsnp_flat.txt
t/data/delimitedline_test.txt
t/data/dmel-4-chromosome-r5.46.fasta
t/data/dmel-4-r5.24.no_gff_version.gff
t/data/dmel-4-r5.24.partial.gff
t/data/dmel-4-r5.27_exon_IDS.txt
t/data/dmel-4-r5.46.genes.gff
t/data/dmel-4-r5.46.genes.partial.gff
t/data/dmel-4-r5.46.gff
t/data/dmel-4-r5.46.no_UTR.gff
t/data/Dmel_genes_4.gff
t/data/ds_ch1.short.xml
t/data/ensemble_01_short.gtf
t/data/ensemble_01_short.valid.gff3
t/data/ensGene_hg19_chr22.txt
t/data/exon_hunter.short.gtf
t/data/exon_hunter.short.valid.gff3
t/data/fasta_ant/directory.index
t/data/fasta_ant/lhum_genome_4.0_short.fasta
t/data/fasta_hg18/chr22_hg18.fasta
t/data/file1.txt
t/data/file2.txt
t/data/gal_feature_test.sqlite
t/data/gencode_short.gtf
t/data/gencode_short.valid.gff3
t/data/gff_tool_map_seqids.txt
t/data/gff_tool_validate.txt
t/data/gvf_pragma_template_hg18.txt
t/data/gvf_pragma_template_hg19.txt
t/data/hapmap_genotypes.txt
t/data/hg18_chr22.fa
t/data/hg19_chr22.fa
t/data/Homo_sapiens.GRCh37.73.chr22.short.gff3.gz
t/data/Homo_sapiens_1005.short.gtf
t/data/Homo_sapiens_1005.short.valid.gff3
t/data/hsap_hg18.short.gtf
t/data/hsap_hg18.short.valid.gff3
t/data/interval_1.gff
t/data/interval_2.gff
t/data/interval_3.gff
t/data/knownGene_hg19_chr22.txt
t/data/korean_indel.gff
t/data/korean_snp.gff
t/data/macs_summits.bed
t/data/map_seqids.gff
t/data/map_seqids.txt
t/data/maq_cns2snp.snp
t/data/multi_fasta.fa
t/data/NA12878.annovar_input_short.exonic_variant_function
t/data/na18507_sanger_indel.gff
t/data/NG_027806.1.gff3
t/data/NM_001033828.1.gff3
t/data/NR_036541.1.gff3
t/data/quake_snp.txt
t/data/refGene_hg19_chr22.txt
t/data/refgene_short.gtf
t/data/refgene_short.valid.gff3
t/data/refseq_chr22.trim.gff3
t/data/remove_ids.txt
t/data/samtools_pileup.txt
t/data/set_ops_01.gff
t/data/set_ops_02.gff
t/data/set_ops_03.gff
t/data/smith_ant_snps.gff
t/data/snv_minimal_chr22.gvf
t/data/soap_indel.gff
t/data/soap_snp.gff
t/data/soap_snp.txt
t/data/solid.txt
t/data/solid_snp.txt
t/data/SRR043167.indel.vcf
t/data/template.gff
t/data/template_sequence_alteration.gff
t/data/test.vcf
t/data/test_blend1.gvf
t/data/test_blend2.gvf
t/data/test_blend3.gvf
t/data/trait_o_matic.gff
t/data/twinscan_chr1.short.gtf
t/data/twinscan_chr1.short.valid.gff3
t/data/unknown_01_short.gtf
t/data/unknown_01_short.valid.gff3
t/data/vegaGene_hg19_chr22.txt
t/data/venter_indel.gff
t/data/venter_snp.gff
t/data/watson_cshl.txt
t/data/wgEncodeGencodeManualV4_hg19_chr22.txt
t/gal_test_all.t