LICENSE
README.md
setup.py
gAIRR_suite/__init__.py
gAIRR_suite/gAIRR_annotate.py
gAIRR_suite/gAIRR_call.py
gAIRR_suite.egg-info/PKG-INFO
gAIRR_suite.egg-info/SOURCES.txt
gAIRR_suite.egg-info/dependency_links.txt
gAIRR_suite.egg-info/entry_points.txt
gAIRR_suite.egg-info/not-zip-safe
gAIRR_suite.egg-info/requires.txt
gAIRR_suite.egg-info/top_level.txt
gAIRR_suite/material/BCRD_alleles_parsed.fasta
gAIRR_suite/material/BCRD_plusHep_alleles_parsed.fasta
gAIRR_suite/material/BCRD_plusHep_alleles_parsed.fasta.amb
gAIRR_suite/material/BCRD_plusHep_alleles_parsed.fasta.ann
gAIRR_suite/material/BCRD_plusHep_alleles_parsed.fasta.bwt
gAIRR_suite/material/BCRD_plusHep_alleles_parsed.fasta.pac
gAIRR_suite/material/BCRD_plusHep_alleles_parsed.fasta.sa
gAIRR_suite/material/BCRJ_alleles_parsed.fasta
gAIRR_suite/material/BCRJ_alleles_parsed.fasta.amb
gAIRR_suite/material/BCRJ_alleles_parsed.fasta.ann
gAIRR_suite/material/BCRJ_alleles_parsed.fasta.bwt
gAIRR_suite/material/BCRJ_alleles_parsed.fasta.pac
gAIRR_suite/material/BCRJ_alleles_parsed.fasta.sa
gAIRR_suite/material/BCRV_alleles.fasta
gAIRR_suite/material/BCRV_alleles_parsed.fasta
gAIRR_suite/material/BCRV_alleles_parsed.fasta.amb
gAIRR_suite/material/BCRV_alleles_parsed.fasta.ann
gAIRR_suite/material/BCRV_alleles_parsed.fasta.bwt
gAIRR_suite/material/BCRV_alleles_parsed.fasta.fai
gAIRR_suite/material/BCRV_alleles_parsed.fasta.pac
gAIRR_suite/material/BCRV_alleles_parsed.fasta.sa
gAIRR_suite/material/HG001_IGHV_annotation.txt
gAIRR_suite/material/IGHV3-30_genes_rename.fasta
gAIRR_suite/material/IGHV_functional.txt
gAIRR_suite/material/IGH_functional.txt
gAIRR_suite/material/IGJ.txt
gAIRR_suite/material/IGKV_functional.txt
gAIRR_suite/material/IGLV_functional.txt
gAIRR_suite/material/IG_RSS.fasta
gAIRR_suite/material/IG_heptamer_nonamer.fasta
gAIRR_suite/material/TCRD_alleles_parsed.fasta
gAIRR_suite/material/TCRD_plusHep_alleles_parsed.fasta
gAIRR_suite/material/TCRD_plusHep_alleles_parsed.fasta.amb
gAIRR_suite/material/TCRD_plusHep_alleles_parsed.fasta.ann
gAIRR_suite/material/TCRD_plusHep_alleles_parsed.fasta.bwt
gAIRR_suite/material/TCRD_plusHep_alleles_parsed.fasta.pac
gAIRR_suite/material/TCRD_plusHep_alleles_parsed.fasta.sa
gAIRR_suite/material/TCRJ_alleles_parsed.fasta
gAIRR_suite/material/TCRJ_alleles_parsed.fasta.amb
gAIRR_suite/material/TCRJ_alleles_parsed.fasta.ann
gAIRR_suite/material/TCRJ_alleles_parsed.fasta.bwt
gAIRR_suite/material/TCRJ_alleles_parsed.fasta.pac
gAIRR_suite/material/TCRJ_alleles_parsed.fasta.sa
gAIRR_suite/material/TCRV_alleles.fasta
gAIRR_suite/material/TCRV_alleles_parsed.fasta
gAIRR_suite/material/TCRV_alleles_parsed.fasta.amb
gAIRR_suite/material/TCRV_alleles_parsed.fasta.ann
gAIRR_suite/material/TCRV_alleles_parsed.fasta.bwt
gAIRR_suite/material/TCRV_alleles_parsed.fasta.pac
gAIRR_suite/material/TCRV_alleles_parsed.fasta.sa
gAIRR_suite/material/TRAV_functional.txt
gAIRR_suite/material/TRBV_functional.txt
gAIRR_suite/material/TRGV_functional.txt
gAIRR_suite/material/TR_RSS.fasta
gAIRR_suite/material/TR_heptamer_nonamer.fasta
gAIRR_suite/material/__init__.py
gAIRR_suite/material/HPRCv1_plus/BCRD_plusHep_alleles_parsed.fasta
gAIRR_suite/material/HPRCv1_plus/BCRJ_alleles_parsed.fasta
gAIRR_suite/material/HPRCv1_plus/BCRV_alleles_parsed.fasta
gAIRR_suite/material/HPRCv1_plus/IGH_functional.txt
gAIRR_suite/material/HPRCv1_plus/TCRD_plusHep_alleles_parsed.fasta
gAIRR_suite/material/HPRCv1_plus/TCRJ_alleles_parsed.fasta
gAIRR_suite/material/HPRCv1_plus/TCRV_alleles_parsed.fasta
gAIRR_suite/material/HPRCv1_plus/__init__.py
gAIRR_suite/scripts/AIRRAnnotate.2.sh
gAIRR_suite/scripts/AIRRAnnotate.sh
gAIRR_suite/scripts/AIRRCall.2.sh
gAIRR_suite/scripts/AIRRCall.sh
gAIRR_suite/scripts/AIRRVerify.sh
gAIRR_suite/scripts/__init__.py
gAIRR_suite/scripts/allele_calling.sh
gAIRR_suite/scripts/allele_consensus.py
gAIRR_suite/scripts/allele_consensus.sh
gAIRR_suite/scripts/alternative_contig.sh
gAIRR_suite/scripts/analyze_read_depth_with_bwa.py
gAIRR_suite/scripts/annotation_locus_parser.py
gAIRR_suite/scripts/annotation_with_asm.py
gAIRR_suite/scripts/annotation_with_asm.sh
gAIRR_suite/scripts/assembly_1st_round.sh
gAIRR_suite/scripts/assembly_2nd_round.sh
gAIRR_suite/scripts/assembly_analysis.sh
gAIRR_suite/scripts/batch_AIRRAnnotate.sh
gAIRR_suite/scripts/blastn.sh
gAIRR_suite/scripts/build_pwm.py
gAIRR_suite/scripts/calling_threshold.py
gAIRR_suite/scripts/check_RSS.sh
gAIRR_suite/scripts/check_RSS_1st_scan.py
gAIRR_suite/scripts/check_RSS_2nd_scan.py
gAIRR_suite/scripts/check_contig_RSS.sh
gAIRR_suite/scripts/clustalw.sh
gAIRR_suite/scripts/collect_novel_alleles.py
gAIRR_suite/scripts/compare_annotation.py
gAIRR_suite/scripts/compare_with_annotation.py
gAIRR_suite/scripts/copy_1st_contig.py
gAIRR_suite/scripts/coverage_analysis.py
gAIRR_suite/scripts/coverage_edit.Rmd
gAIRR_suite/scripts/database_collect.sh
gAIRR_suite/scripts/denovo_backbone.sh
gAIRR_suite/scripts/exact_filter.sh
gAIRR_suite/scripts/fastq2fasta.sh
gAIRR_suite/scripts/fetch_annotated_allele.py
gAIRR_suite/scripts/fetch_chromosome.py
gAIRR_suite/scripts/fetch_reads_alleles.py
gAIRR_suite/scripts/fetch_sam.py
gAIRR_suite/scripts/fetch_support_reads.py
gAIRR_suite/scripts/filter_corrected_alleles.py
gAIRR_suite/scripts/find_rss.py
gAIRR_suite/scripts/flanking_coverage.py
gAIRR_suite/scripts/flanking_sequence.sh
gAIRR_suite/scripts/get_allele_length.py
gAIRR_suite/scripts/get_annotated.sh
gAIRR_suite/scripts/get_asm_flanking.py
gAIRR_suite/scripts/group_allele_reads.py
gAIRR_suite/scripts/haplotype_analysis.sh
gAIRR_suite/scripts/locus.py
gAIRR_suite/scripts/merge_novel_alleles.py
gAIRR_suite/scripts/merge_novel_alleles.sh
gAIRR_suite/scripts/novel_allele.py
gAIRR_suite/scripts/novel_allele.sh
gAIRR_suite/scripts/output_reads.py
gAIRR_suite/scripts/parse_blastn_output.py
gAIRR_suite/scripts/parse_bwa_sam.py
gAIRR_suite/scripts/parse_cluster_realign.py
gAIRR_suite/scripts/parse_cluster_realign2.py
gAIRR_suite/scripts/parse_contig_realign.py
gAIRR_suite/scripts/parse_sam_haplotyping.py
gAIRR_suite/scripts/parse_tree.py
gAIRR_suite/scripts/plot_allele_len.py
gAIRR_suite/scripts/plot_tree.r
gAIRR_suite/scripts/plotting.Rmd
gAIRR_suite/scripts/process_rss_for_grep.py
gAIRR_suite/scripts/shrink_sam_to_range.py
gAIRR_suite/scripts/test_path.sh
gAIRR_suite/scripts/utils.py
gAIRR_suite/scripts/verify_flanking_region_bwa.py
gAIRR_suite/scripts/verify_novel_alleles.py
gAIRR_suite/scripts/analysis/__init__.py
gAIRR_suite/scripts/analysis/bed_generator.py
gAIRR_suite/scripts/analysis/check_duplicates.py
gAIRR_suite/scripts/analysis/collect_gene_from_annotation.py
gAIRR_suite/scripts/analysis/collect_gene_from_bed.py
gAIRR_suite/scripts/analysis/collect_gene_from_read_depth.py
gAIRR_suite/scripts/analysis/compare_2_annotation.py
gAIRR_suite/scripts/analysis/compare_call_and_annotation.py
gAIRR_suite/scripts/analysis/correct_annotation_D_heptamer.py
gAIRR_suite/scripts/analysis/extract_functional.py
gAIRR_suite/scripts/analysis/utils.py