bin/CHANGELOG.md
bin/CITATION.bib
bin/CONTRIBUTORS.md
bin/IRMA
bin/IRMA_RES/defaults.sh
bin/IRMA_RES/modules/CoV/config/CoV.sh
bin/IRMA_RES/modules/CoV/config/elongate.sh
bin/IRMA_RES/modules/CoV/config/fast.sh
bin/IRMA_RES/modules/CoV/config/grid.sh
bin/IRMA_RES/modules/CoV/config/illumina-2x100.sh
bin/IRMA_RES/modules/CoV/config/illumina-2x50.sh
bin/IRMA_RES/modules/CoV/config/illumina-se.sh
bin/IRMA_RES/modules/CoV/config/minimap2.sh
bin/IRMA_RES/modules/CoV/config/minion-long-reads-notmp.sh
bin/IRMA_RES/modules/CoV/config/minion-long-reads.sh
bin/IRMA_RES/modules/CoV/config/minion-sensitive.sh
bin/IRMA_RES/modules/CoV/config/molecular-loop-illumina.sh
bin/IRMA_RES/modules/CoV/config/pacbio.sh
bin/IRMA_RES/modules/CoV/config/permissive.sh
bin/IRMA_RES/modules/CoV/config/pgm-hq.sh
bin/IRMA_RES/modules/CoV/config/pgm.sh
bin/IRMA_RES/modules/CoV/config/recombinant-a2m.sh
bin/IRMA_RES/modules/CoV/config/recombinant.sh
bin/IRMA_RES/modules/CoV/config/ref.sh
bin/IRMA_RES/modules/CoV/config/roche.sh
bin/IRMA_RES/modules/CoV/config/s-gene-pacbio.sh
bin/IRMA_RES/modules/CoV/config/s-gene.sh
bin/IRMA_RES/modules/CoV/config/sensitive.sh
bin/IRMA_RES/modules/CoV/init.sh
bin/IRMA_RES/modules/CoV/primers/README.txt
bin/IRMA_RES/modules/CoV/primers/V1_ARTIC.txt
bin/IRMA_RES/modules/CoV/primers/V2_ARTIC.txt
bin/IRMA_RES/modules/CoV/primers/V3_ARTIC.txt
bin/IRMA_RES/modules/CoV/profiles/MERS-CoV_hmm.mod
bin/IRMA_RES/modules/CoV/profiles/SARS-CoV-2-mCherry_hmm.mod
bin/IRMA_RES/modules/CoV/profiles/SARS-CoV-2-mNG_hmm.mod
bin/IRMA_RES/modules/CoV/profiles/SARS-CoV-2_hmm.mod
bin/IRMA_RES/modules/CoV/profiles/instructions_for_profiles.txt
bin/IRMA_RES/modules/CoV/reference/SARS-CoV-2_recombinant.fasta
bin/IRMA_RES/modules/CoV/reference/SARS-CoV-2_spike.fasta
bin/IRMA_RES/modules/CoV/reference/consensus.fasta
bin/IRMA_RES/modules/CoV/reference/insructions_for_references.txt
bin/IRMA_RES/modules/EBOLA/config/EBOLA-fast.sh
bin/IRMA_RES/modules/EBOLA/config/EBOLA.sh
bin/IRMA_RES/modules/EBOLA/init.sh
bin/IRMA_RES/modules/EBOLA/profiles/CIEBOV_hmm.mod
bin/IRMA_RES/modules/EBOLA/profiles/EBOV_BDBV_hmm.mod
bin/IRMA_RES/modules/EBOLA/profiles/LLOV_hmm.mod
bin/IRMA_RES/modules/EBOLA/profiles/MARV_hmm.mod
bin/IRMA_RES/modules/EBOLA/profiles/REBOV_hmm.mod
bin/IRMA_RES/modules/EBOLA/profiles/SEBOV_hmm.mod
bin/IRMA_RES/modules/EBOLA/profiles/ZEBOV_hmm.mod
bin/IRMA_RES/modules/EBOLA/reference/consensus.fasta
bin/IRMA_RES/modules/FLU/config/FLU-alt.sh
bin/IRMA_RES/modules/FLU/config/FLU-avian-residual.sh
bin/IRMA_RES/modules/FLU/config/FLU-avian.sh
bin/IRMA_RES/modules/FLU/config/FLU-fast.sh
bin/IRMA_RES/modules/FLU/config/FLU-lowQC.sh
bin/IRMA_RES/modules/FLU/config/FLU-minion.sh
bin/IRMA_RES/modules/FLU/config/FLU-pacbio.sh
bin/IRMA_RES/modules/FLU/config/FLU-pgm.sh
bin/IRMA_RES/modules/FLU/config/FLU-ref.sh
bin/IRMA_RES/modules/FLU/config/FLU-roche.sh
bin/IRMA_RES/modules/FLU/config/FLU-secondary.sh
bin/IRMA_RES/modules/FLU/config/FLU-sensitive.sh
bin/IRMA_RES/modules/FLU/config/FLU-utr.sh
bin/IRMA_RES/modules/FLU/config/FLU.sh
bin/IRMA_RES/modules/FLU/init.sh
bin/IRMA_RES/modules/FLU/profiles/A_HA_H10_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H11_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H12_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H13_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H14_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H15_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H16_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H1_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H2_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H3_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H4_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H5_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H6_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H7_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H8_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_HA_H9_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_MP_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N1_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N2_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N3_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N4_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N5_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N6_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N7_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N8_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NA_N9_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NP_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_NS_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_PA_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_PB1_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/A_PB2_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_HA_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_MP_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_NA_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_NP_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_NS_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_PA_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_PB1_hmm.mod
bin/IRMA_RES/modules/FLU/profiles/B_PB2_hmm.mod
bin/IRMA_RES/modules/FLU/reference/consensus.fasta
bin/IRMA_RES/modules/FLU/reference/description.txt
bin/IRMA_RES/modules/FLU_AD/config/fast.sh
bin/IRMA_RES/modules/FLU_AD/config/grid.sh
bin/IRMA_RES/modules/FLU_AD/config/lowQC.sh
bin/IRMA_RES/modules/FLU_AD/config/pacbio.sh
bin/IRMA_RES/modules/FLU_AD/config/pgm.sh
bin/IRMA_RES/modules/FLU_AD/config/ref.sh
bin/IRMA_RES/modules/FLU_AD/config/roche.sh
bin/IRMA_RES/modules/FLU_AD/config/utr.sh
bin/IRMA_RES/modules/FLU_AD/init.sh
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H10_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H11_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H12_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H13_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H14_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H15_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H16_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H1_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H2_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H3_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H4_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H5_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H6_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H7_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H8_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_HA_H9_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_MP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N1_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N2_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N3_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N4_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N5_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N6_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N7_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N8_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NA_N9_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_NS_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_PA_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_PB1_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/A_PB2_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_HA_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_MP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_NA_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_NP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_NS_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_PA_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_PB1_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/B_PB2_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/C_HE_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/C_MP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/C_NP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/C_NS_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/C_P3_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/C_PB1_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/C_PB2_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/D_HE_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/D_MP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/D_NP_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/D_NS_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/D_P3_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/D_PB1_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/D_PB2_hmm.mod
bin/IRMA_RES/modules/FLU_AD/profiles/instructions_for_profiles.txt
bin/IRMA_RES/modules/FLU_AD/reference/consensus.fasta
bin/IRMA_RES/modules/FLU_AD/reference/consensus_AB.fasta
bin/IRMA_RES/modules/FLU_AD/reference/consensus_CD.fasta
bin/IRMA_RES/modules/FLU_AD/reference/insructions_for_references.txt
bin/IRMA_RES/modules/RSV/ACKNOWLEDGEMENTS.md
bin/IRMA_RES/modules/RSV/config/RSV-pacbio.sh
bin/IRMA_RES/modules/RSV/config/RSV-ref.sh
bin/IRMA_RES/modules/RSV/config/RSV.sh
bin/IRMA_RES/modules/RSV/config/minion.sh
bin/IRMA_RES/modules/RSV/init.sh
bin/IRMA_RES/modules/RSV/profiles/RSV_AD_hmm.mod
bin/IRMA_RES/modules/RSV/profiles/RSV_A_hmm.mod
bin/IRMA_RES/modules/RSV/profiles/RSV_BD_hmm.mod
bin/IRMA_RES/modules/RSV/profiles/RSV_B_hmm.mod
bin/IRMA_RES/modules/RSV/reference/consensus.fasta
bin/IRMA_RES/scripts/a2mToMatchStats.pl
bin/IRMA_RES/scripts/amendConsensus.pl
bin/IRMA_RES/scripts/amplicon_dropout_pad.pl
bin/IRMA_RES/scripts/call.pl
bin/IRMA_RES/scripts/catSAMfiles.pl
bin/IRMA_RES/scripts/combineALIGNstats.pl
bin/IRMA_RES/scripts/combineSAMstats.pl
bin/IRMA_RES/scripts/completeMatrix.pl
bin/IRMA_RES/scripts/coverageDiagram.R
bin/IRMA_RES/scripts/deprecated_or_removed.sh
bin/IRMA_RES/scripts/disk_check.pl
bin/IRMA_RES/scripts/finalRefs.pl
bin/IRMA_RES/scripts/getPairingStats.pl
bin/IRMA_RES/scripts/heuristicDiagram.R
bin/IRMA_RES/scripts/interleavedSamples.pl
bin/IRMA_RES/scripts/irma-core_Darwin
bin/IRMA_RES/scripts/irma-core_Linux_aarch64
bin/IRMA_RES/scripts/irma-core_Linux_x86_64
bin/IRMA_RES/scripts/leftjoin.pl
bin/IRMA_RES/scripts/makePatchworkConsensus.pl
bin/IRMA_RES/scripts/makePluralityConsensus.pl
bin/IRMA_RES/scripts/ordinalHeaders.pl
bin/IRMA_RES/scripts/parseBlat.pl
bin/IRMA_RES/scripts/parseSORTresults.pl
bin/IRMA_RES/scripts/partitionByField.pl
bin/IRMA_RES/scripts/percentages.R
bin/IRMA_RES/scripts/phase.pl
bin/IRMA_RES/scripts/run_config.sh
bin/IRMA_RES/scripts/run_info.sh
bin/IRMA_RES/scripts/samStats.pl
bin/IRMA_RES/scripts/sanitize_shell_configs.pl
bin/IRMA_RES/scripts/scoreSAM.pl
bin/IRMA_RES/scripts/selectSequences.pl
bin/IRMA_RES/scripts/simpleCoverageDiagram.R
bin/IRMA_RES/scripts/sqmHeatmap.R
bin/IRMA_RES/scripts/sumField.pl
bin/IRMA_RES/scripts/varCallStats.pl
bin/IRMA_RES/scripts/vcfGenerator.pl
bin/IRMA_RES/scripts/winnowSAM.pl
bin/IRMA_RES/third_party/MANIFEST.md
bin/IRMA_RES/third_party/packaged-citations-licenses/ssw-license.txt
bin/IRMA_RES/third_party/packaged-citations-licenses/ssw-modified-make.sh
bin/IRMA_RES/third_party/ssw_Darwin
bin/IRMA_RES/third_party/ssw_Linux_aarch64
bin/IRMA_RES/third_party/ssw_Linux_x86_64
bin/LABEL
bin/LABEL_RES/scripts/buildDataMatrix.pl
bin/LABEL_RES/scripts/doLABELlevel.pl
bin/LABEL_RES/scripts/evaluateResults.pl
bin/LABEL_RES/scripts/fastaExtractor.pl
bin/LABEL_RES/scripts/finalizeResults.pl
bin/LABEL_RES/scripts/findByNamePostOrder.pl
bin/LABEL_RES/scripts/interleavedSamples.pl
bin/LABEL_RES/scripts/parseScores.pl
bin/LABEL_RES/scripts/partitionTaxa.pl
bin/LABEL_RES/scripts/removeByRedundantHeader.pl
bin/LABEL_RES/scripts/removeGapColumns.pl
bin/LABEL_RES/scripts/reviseTaxa.pl
bin/LABEL_RES/scripts/stripSequences.pl
bin/LABEL_RES/third_party/MANIFEST.md
bin/LABEL_RES/third_party/align2model_Darwin
bin/LABEL_RES/third_party/align2model_Linux_aarch64
bin/LABEL_RES/third_party/align2model_Linux_x86_64
bin/LABEL_RES/third_party/copyright_and_licenses/sam3.5/COPYRIGHT.txt
bin/LABEL_RES/third_party/copyright_and_licenses/sam3.5/README.txt
bin/LABEL_RES/third_party/copyright_and_licenses/sam3.5/SAM Redistribution Special Permissions.pdf
bin/LABEL_RES/third_party/copyright_and_licenses/shogun1.1.0_cmdline_static/gpl-3.0.txt
bin/LABEL_RES/third_party/copyright_and_licenses/shogun1.1.0_cmdline_static/mac_configure.txt
bin/LABEL_RES/third_party/hmmscore_Darwin
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bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N2_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N3_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N4_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N5_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N6_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N7_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N8_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NA_N9_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NP_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_NS_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_PA_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_PB1_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/A_PB2_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_HA_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_MP_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_NA_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_NP_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_NS_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_PA_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_PB1_hmm.mod
bin/LABEL_RES/training_data/irma-FLU/x-rev/B_PB2_hmm.mod
bin/LICENSE
bin/README.md
bin/alignPositionByPSA.pl
bin/annotateSubstitutions.pl
bin/augmentSampleResults.pl
bin/build_env_setup.sh
bin/conda_build.sh
bin/metadata_conda_debug.yaml
