../../../bin/PACU,sha256=jBBKRqQDtguBiaDDUv9WJ0BN0_guTKQOL2Cvkf3bdTg,468
../../../bin/PACU_galaxy,sha256=5qv6naWeI9fF5uw43DcKM9R6wAOkYbhUDpvuvkcliD4,466
../../../bin/PACU_map,sha256=lC_f1rymDkBK-IR3L9Ie9rFX5I0lcSnY6B2yjhvb5Xw,470
pacu/__init__.py,sha256=jlaoP_IY-yBxM21N6L9zJkOivLkqvot_K1XrRkjnFtI,8788
pacu/__pycache__/__init__.cpython-314.pyc,,
pacu/__pycache__/galaxy.cpython-314.pyc,,
pacu/__pycache__/map_to_ref.cpython-314.pyc,,
pacu/__pycache__/run_pacu.cpython-314.pyc,,
pacu/__pycache__/version.cpython-314.pyc,,
pacu/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
pacu/app/__pycache__/__init__.cpython-314.pyc,,
pacu/app/__pycache__/command.cpython-314.pyc,,
pacu/app/command.py,sha256=uLeMBvYZ0SGGPo5A749p4exmnSyTVWjKS87E0uPvVYM,2749
pacu/app/report/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
pacu/app/report/__pycache__/__init__.cpython-314.pyc,,
pacu/app/report/__pycache__/htmlbase.cpython-314.pyc,,
pacu/app/report/__pycache__/htmlcitation.cpython-314.pyc,,
pacu/app/report/__pycache__/htmlelement.cpython-314.pyc,,
pacu/app/report/__pycache__/htmlreport.cpython-314.pyc,,
pacu/app/report/__pycache__/htmlreportsection.cpython-314.pyc,,
pacu/app/report/__pycache__/htmltablecell.cpython-314.pyc,,
pacu/app/report/htmlbase.py,sha256=GYOX6EPtfs0vo7K1oyXNYDaO_EXhYWfjxcaoPpGeCio,7662
pacu/app/report/htmlcitation.py,sha256=eCarrDh53FNTS7LfEPLytvAXLAx9WPEWzb5VSpYhbm0,3204
pacu/app/report/htmlelement.py,sha256=Fs-qhqBUdaF1c_v1PrIcS4yyEbVaCcHwyLGPqKUlrB4,2420
pacu/app/report/htmlreport.py,sha256=Zn3fN0wKTqsDMWeJEwAQneygi3pO7kHwiI408F5x8n0,3316
pacu/app/report/htmlreportsection.py,sha256=1cpEtotPjA36ake5s6O6LBV062Fk7WsqlIPHXsJdlcI,4262
pacu/app/report/htmltablecell.py,sha256=cp5II8TDx4iCZZDCL8pKSh2LHt6XPDYmuAzMhLtnTCw,1100
pacu/app/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
pacu/app/utils/__pycache__/__init__.cpython-314.pyc,,
pacu/app/utils/__pycache__/bamutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/bowtie2utils.cpython-314.pyc,,
pacu/app/utils/__pycache__/cliutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/fastaidxutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/iqtreeutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/loggingutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/megautils.cpython-314.pyc,,
pacu/app/utils/__pycache__/reportutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/snakemakeutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/snpmatrixutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/trimmingutils.cpython-314.pyc,,
pacu/app/utils/__pycache__/workflowutils.cpython-314.pyc,,
pacu/app/utils/bamutils.py,sha256=dHXnxHokhXtq-0IswPRXmg8XWxbDoPl6tVggtgbAQHM,2073
pacu/app/utils/bowtie2utils.py,sha256=gO6rgKetAvvOrE_mI7EeMhLpZnrBToeyGNGvM_dHgv0,293
pacu/app/utils/cliutils.py,sha256=aX88wNkbJa-sRQrCC_fBgeGEnnEbsKfw45QkoM_Xugk,286
pacu/app/utils/fastaidxutils.py,sha256=OSDUg20EcA-JCmLxq48jAoy2_PxLFCt8HAnHXnKjuy8,584
pacu/app/utils/iqtreeutils.py,sha256=O3kKubgKleJR2JPvEyAzzfkcGa-85jd_LhpZU4QNdyk,1468
pacu/app/utils/loggingutils.py,sha256=0gzFZkJsbsdRA7V2Ip4CflCLS7MEPemWEgsIxBiGauI,806
pacu/app/utils/megautils.py,sha256=sDQ-SJmS4Dg9mLz1yOOwfSR3SFKNSyYg6UMX50ezDZs,7707
pacu/app/utils/reportutils.py,sha256=1NG2j_pM3p0rtC5W33LLKm9l0IeO2lcTZ9lpJGj__vM,9828
pacu/app/utils/snakemakeutils.py,sha256=Yyc9psW1B5N6T_ETO1IyTFivcjvl2hLK0GQ18asL94U,2362
pacu/app/utils/snpmatrixutils.py,sha256=ztdoS5QaJv76yjtOaJAfAyiOYtmKXJJnP5AjVIYAmeY,3987
pacu/app/utils/trimmingutils.py,sha256=Qyi2m2PSQ5Uu1duAUv3qd-waberD_YeMD9XdbOgHC0Q,1488
pacu/app/utils/workflowutils.py,sha256=71HwoehvBFbhKvhEvPlTshYh8eLQUeNC90z3avKml_I,10010
pacu/galaxy.py,sha256=HcAkHT6zmNKBgE1CRIxWEsE4cICh6oa-MVTSzrBNgNY,3352
pacu/map_to_ref.py,sha256=PiWGKdXAI6MpWGa444keM2fp1EdlGtCkIiU8HYg7yZE,13162
pacu/resources/citations/Bogaerts_2023-ont_outbreak.json,sha256=CM07K__XeWFoE9FjYTxRu6kPcRGz0DqEgAGfqMUQ15A,794
pacu/resources/citations/Croucher_2015-gubbins.json,sha256=v_8zsK2nIAsM0aMMTTjpvHMx0r-RzDKg_pR_41GnYbQ,604
pacu/resources/citations/Danecek_2021-bcftools.json,sha256=xG42JGjAtaJMs9kUl6TpwGAC6IY97RKWB-GSFaLPdcM,804
pacu/resources/citations/Kalyaanamoorthy_2017-iq_tree_model.json,sha256=kD-zfmt9Dae-veeIz10p_G4yy5UsX1TLL20x7X1wpT8,479
pacu/resources/citations/Kumar_2018-megax.json,sha256=e260A6YL30-JSZdjyMJtElFCx1-c7Wo58RzQMlSaSUA,558
pacu/resources/citations/Li_2018-minimap2.json,sha256=W8WzoPLGgAooZId9ioRvBOX2Uc58OE4nZNLeU-TymR4,360
pacu/resources/citations/Nguyen_2015-iq_tree.json,sha256=gDIx3qiH5BRl4hYJB7UunozOAmMNdj-3EfB3ina5XTU,622
pacu/resources/citations/Quinlan_2010-bedtools.json,sha256=eopQHxfUtDQJsWrxpSuuayFQix4YkXdTpHHeIpSFzq8,406
pacu/resources/figtree_template.txt,sha256=8C14dSS2Bmpyoswsd-dnS5lc2HuD41fsKXeGxMnUYww,3198
pacu/resources/mega/infer_ml_nucleotide_template.mao,sha256=NG7Ow8_BQCBdcux8iZxf9Fj-pbx-rSTfjgfIyOi2apA,2545
pacu/resources/mega/model_sel_ml_nucleotide_template.mao,sha256=T8dCNUp4uFX2d1Ff_YGasLfvFhVsYjtwUVZGSP-gHnk,1636
pacu/resources/snp_workflow.smk,sha256=okE-oT7JK-IIPc6H_CGm26hxslVqtVjvpln4j18JiaY,31610
pacu/resources/style.css,sha256=3JzU596nVninJuVG0ouFidWWNtqW3Knt-qBQzQ95BII,3733
pacu/resources/testdata/NC_002695.2-subset.fasta,sha256=3yl8o6xbM6Y9MA7FO3kRHujqxEFtwg_JEoH7xS6g3ls,10931
pacu/resources/testdata/bam/ilmn/TIAC1151.bam,sha256=aYKJqejbz3XreQML_VqqdDtQP8n_d4LrE0jtJMtMn44,200748
pacu/resources/testdata/bam/ilmn/TIAC1151.bam.bai,sha256=STimMqmjiNpCXGZ4-GiCSkuKB2YJu2wmiByw43Obi8s,96
pacu/resources/testdata/bam/ilmn/TIAC1153.bam,sha256=ldEeH5hNuvED-5yvACkF72ELSTXYgnRPjAxsCX3aDTU,239563
pacu/resources/testdata/bam/ilmn/TIAC1153.bam.bai,sha256=td3dD3lOwWlQw6U5V9JoPeELU1_hfOJsRg5f141kTFk,96
pacu/resources/testdata/bam/ilmn/TIAC1660.bam,sha256=lsduiktPVsKaWCdiFOuOKf1fJ0W11vtnyf8VaDP9UYk,278504
pacu/resources/testdata/bam/ilmn/TIAC1660.bam.bai,sha256=UePoDLuU8LZjxGmD4Q6Jl_VavezdD4mJUmuVLA9k7f8,96
pacu/resources/testdata/bam/ont/TIAC1151-R10-ds.bam,sha256=mJvfEPCyc9pN8bKF_0PCAgrHfQSsTrd4ep7UkPD7V28,371825
pacu/resources/testdata/bam/ont/TIAC1151-R10-ds.bam.bai,sha256=FXPg2YOfJOPw3sjs01R91U8n3SrOK7mBTyqCoYRuCII,96
pacu/resources/testdata/bam/ont/TIAC1638-R9-ds.bam,sha256=PFZfRZI4DYjgeO2V5IFbhrER4oV7z4f02R-ASOh5gtw,357428
pacu/resources/testdata/bam/ont/TIAC1638-R9-ds.bam.bai,sha256=OEd6vEoGJg4d3dyD3MX5vwiqFah0eYH5cYUHMq-U1zg,96
pacu/resources/testdata/fastq/TIAC1151-ont.fastq.gz,sha256=9OyJ11BUKomr-po-D_iHXxtdKqX7V86ldUjYjwn_Fl4,374774
pacu/resources/testdata/fastq/TIAC1151_1P.fastq.gz,sha256=z-6zQ3sY-BBWJ5f03feEjkN7WPXJI7LNScBnJanThVo,2251
pacu/resources/testdata/fastq/TIAC1151_2P.fastq.gz,sha256=YR2vdeCvtzOhOb83arhHAm59AHpKU-oK-4A5ycmuJVA,2417
pacu/resources/testdata/mega/model_selection_output.csv,sha256=23ZgJyJjl70a8O7Q_d5T-dtxFgpZQWv75-JOUOH5c14,5023
pacu/resources/testdata/phylogeny.nwk,sha256=wAABF_iQWyrtgKSxRX6UPUk-N034emLdytc_PTQrzRk,103
pacu/resources/testdata/snp_matrix.fasta,sha256=He6NsZ3DqZRvbBAXYVfcXWImrfxgW-bvE1bbU8BHtaI,4253
pacu/resources/testdata/vcfs/TIAC1151.vcf,sha256=4VFk-Wpj0fUUgETOnAdSpgN9KLgIkYjUCLwoSblOyM4,62782
pacu/resources/testdata/vcfs/TIAC1152.vcf,sha256=FuK9Slnm_kc87yxtlzqkhUhCjEbBFjsR1uozHuA-bNM,40283
pacu/resources/testdata/vcfs/TIAC1153.vcf,sha256=wr_-JGKTgepI3S5PXcI5hs1GWFfXquJ3JKsQLeEkKQ8,190967
pacu/resources/testdata/vcfs/TIAC1638.vcf,sha256=dEEWPoFsBBSt3YEy6sgkX5aX1BOUhiPCQF9JlRqh4X8,143331
pacu/run_pacu.py,sha256=Vit97BHlRFReVM6Yd_YIB_u7ruMQRrr021qHxtjhalM,304
pacu/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
pacu/tests/__pycache__/__init__.cpython-314.pyc,,
pacu/tests/__pycache__/test_bamutils.cpython-314.pyc,,
pacu/tests/__pycache__/test_iqtreeutils.cpython-314.pyc,,
pacu/tests/__pycache__/test_map_to_ref.cpython-314.pyc,,
pacu/tests/__pycache__/test_megautils.cpython-314.pyc,,
pacu/tests/__pycache__/test_snpmatrixutils.cpython-314.pyc,,
pacu/tests/__pycache__/test_workflow.cpython-314.pyc,,
pacu/tests/__pycache__/test_workflowutils.cpython-314.pyc,,
pacu/tests/test_bamutils.py,sha256=__AKGARlFXhCEuhZ8gSFs0dyWaeoSNnG2rPPeMcjRzE,978
pacu/tests/test_iqtreeutils.py,sha256=QdDxSrCUIoe63HAiCpUM_GYl1-ZUzl9pPewlfHRM-M4,1146
pacu/tests/test_map_to_ref.py,sha256=RqORTYjxeANjrjakbAOe_SSOSCzLdIHmOZWFBHIziCM,5373
pacu/tests/test_megautils.py,sha256=nUqwx9MmP6qJKRD_3Ae793EiDTbwVB7ABoALRjKJH_Q,2408
pacu/tests/test_snpmatrixutils.py,sha256=QfuIEgusUQN1J6N1Fm62Y4YX1DkRSQaBIbma28u-GyU,2580
pacu/tests/test_workflow.py,sha256=gNXbT3DqmsPbsRu5cTZ27oCgbE2R6c9W8Z1Q7gfvb-o,2635
pacu/tests/test_workflowutils.py,sha256=WD-B-VUjaXh1CJMd5mw_sZSvNSyH7rfL_bItiBXnly0,3120
pacu/version.py,sha256=crlYURA_2Ujkpz7iVPHovvxZRtvt4QBXF5AAFJzRfz0,23
pacu_snp-1.0.0.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4
pacu_snp-1.0.0.dist-info/METADATA,sha256=uCWsuW8AIaKNCgqRkUQog2yD2743x41soEYTXXFBgGE,7084
pacu_snp-1.0.0.dist-info/RECORD,,
pacu_snp-1.0.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
pacu_snp-1.0.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
pacu_snp-1.0.0.dist-info/direct_url.json,sha256=zDfAkH64Gchl4x4gwD1suF4gNjodS5vsb9oniqmKzHU,82
pacu_snp-1.0.0.dist-info/entry_points.txt,sha256=7uT8yR-73f9BVf2U7pkMXBzJ0tzlj6K3Z6Mi4nbOMKw,107
pacu_snp-1.0.0.dist-info/licenses/LICENSE,sha256=xTplwv1WHIfqq_EHLvXcq4ZTBCvBUwhGX1JBNYXrYnE,35146
pacu_snp-1.0.0.dist-info/top_level.txt,sha256=1wQ-zfA_8F5BawXfHotZ8OhQoi6HTv_utWdY-nT-G5A,5
