# HG changeset patch # User iuc # Date 1606514168 0 # Node ID 57dc46adf2da743b2559534f22b3673f55e9d75b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108" diff -r 000000000000 -r 57dc46adf2da flair_collapse.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_collapse.xml Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,188 @@ + + defines high-confidence isoforms from flair-corrected reads + + + flair_macros.xml + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + +
+ +
+ + + + +
+ + + + + + additional_outputs['out_format'] and 'bed' in additional_outputs['out_format'] + + + additional_outputs['out_format'] and 'fasta' in additional_outputs['out_format'] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 57dc46adf2da flair_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_macros.xml Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,60 @@ + + 1.5 + + + flair + + + + + + flair.py --version + + + &1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 && + #else + ln -s '${reference_source_genome.reffile.fields.path}' reference.fa && + #end if + ]]> + + + + + + + + + + + + + + + + + + + + + + +**FLAIR** FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads. +FLAIR can be run optionally with short-read data to help increase splice site accuracy of the long read splice junctions. FLAIR uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data. FLAIR was designed to be able to sense subtle splicing changes in nanopore data from Tang et al. (2018). +It is recommended to combine all samples together prior to running flair-collapse for isoform assembly by concatenating corrected read psl or bed files together. Following the creation of an isoform reference from flair-collapse, consequent steps will assign reads from each sample individually to isoforms of the combined assembly for downstream analyses. + + + + + +Author: Florian Heyl + + + + + 10.1038/s41467-020-15171-6 + + + diff -r 000000000000 -r 57dc46adf2da test-data/UCSC_Main_on_Human_knownGene_region_chrM.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/UCSC_Main_on_Human_knownGene_region_chrM.gtf Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,76 @@ +chrM hg38_knownGene exon 577 647 0.000000 + . gene_id "ENST00000387314.1"; transcript_id "ENST00000387314.1"; +chrM hg38_knownGene exon 648 1601 0.000000 + . gene_id "ENST00000389680.2"; transcript_id "ENST00000389680.2"; +chrM hg38_knownGene exon 1602 1670 0.000000 + . gene_id "ENST00000387342.1"; transcript_id "ENST00000387342.1"; +chrM hg38_knownGene exon 1671 3229 0.000000 + . gene_id "ENST00000387347.2"; transcript_id "ENST00000387347.2"; +chrM hg38_knownGene exon 3230 3304 0.000000 + . gene_id "ENST00000386347.1"; transcript_id "ENST00000386347.1"; +chrM hg38_knownGene start_codon 3307 3309 0.000000 + . gene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; +chrM hg38_knownGene CDS 3307 4259 0.000000 + 0 gene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; +chrM hg38_knownGene stop_codon 4260 4262 0.000000 + . gene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; +chrM hg38_knownGene exon 3307 4262 0.000000 + . gene_id "ENST00000361390.2"; transcript_id "ENST00000361390.2"; +chrM hg38_knownGene exon 4263 4331 0.000000 + . gene_id "ENST00000387365.1"; transcript_id "ENST00000387365.1"; +chrM hg38_knownGene exon 4329 4400 0.000000 - . gene_id "ENST00000387372.1"; transcript_id "ENST00000387372.1"; +chrM hg38_knownGene exon 4402 4469 0.000000 + . gene_id "ENST00000387377.1"; transcript_id "ENST00000387377.1"; +chrM hg38_knownGene start_codon 4470 4472 0.000000 + . gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; +chrM hg38_knownGene CDS 4470 5508 0.000000 + 0 gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; +chrM hg38_knownGene stop_codon 5509 5511 0.000000 + . gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; +chrM hg38_knownGene exon 4470 5511 0.000000 + . gene_id "ENST00000361453.3"; transcript_id "ENST00000361453.3"; +chrM hg38_knownGene exon 5512 5579 0.000000 + . gene_id "ENST00000387382.1"; transcript_id "ENST00000387382.1"; +chrM hg38_knownGene exon 5587 5655 0.000000 - . gene_id "ENST00000387392.1"; transcript_id "ENST00000387392.1"; +chrM hg38_knownGene exon 5657 5729 0.000000 - . gene_id "ENST00000387400.1"; transcript_id "ENST00000387400.1"; +chrM hg38_knownGene exon 5761 5826 0.000000 - . gene_id "ENST00000387405.1"; transcript_id "ENST00000387405.1"; +chrM hg38_knownGene exon 5826 5891 0.000000 - . gene_id "ENST00000387409.1"; transcript_id "ENST00000387409.1"; +chrM hg38_knownGene start_codon 5904 5906 0.000000 + . gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; +chrM hg38_knownGene CDS 5904 7442 0.000000 + 0 gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; +chrM hg38_knownGene stop_codon 7443 7445 0.000000 + . gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; +chrM hg38_knownGene exon 5904 7445 0.000000 + . gene_id "ENST00000361624.2"; transcript_id "ENST00000361624.2"; +chrM hg38_knownGene exon 7446 7514 0.000000 - . gene_id "ENST00000387416.2"; transcript_id "ENST00000387416.2"; +chrM hg38_knownGene exon 7518 7585 0.000000 + . gene_id "ENST00000387419.1"; transcript_id "ENST00000387419.1"; +chrM hg38_knownGene start_codon 7586 7588 0.000000 + . gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; +chrM hg38_knownGene CDS 7586 8266 0.000000 + 0 gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; +chrM hg38_knownGene stop_codon 8267 8269 0.000000 + . gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; +chrM hg38_knownGene exon 7586 8269 0.000000 + . gene_id "ENST00000361739.1"; transcript_id "ENST00000361739.1"; +chrM hg38_knownGene exon 8295 8364 0.000000 + . gene_id "ENST00000387421.1"; transcript_id "ENST00000387421.1"; +chrM hg38_knownGene start_codon 8366 8368 0.000000 + . gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; +chrM hg38_knownGene CDS 8366 8569 0.000000 + 0 gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; +chrM hg38_knownGene stop_codon 8570 8572 0.000000 + . gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; +chrM hg38_knownGene exon 8366 8572 0.000000 + . gene_id "ENST00000361851.1"; transcript_id "ENST00000361851.1"; +chrM hg38_knownGene start_codon 8527 8529 0.000000 + . gene_id "ENST00000361899.2"; transcript_id "ENST00000361899.2"; +chrM hg38_knownGene CDS 8527 9204 0.000000 + 0 gene_id "ENST00000361899.2"; transcript_id "ENST00000361899.2"; +chrM hg38_knownGene stop_codon 9205 9207 0.000000 + . gene_id "ENST00000361899.2"; transcript_id "ENST00000361899.2"; 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203, 0, +chrM 11769 12103 c6e0d5f9-de17-4999-96cf-ba16e130d814;0 51 + 11769 12103 99,99,99 1 334, 0, +chrM 11792 12143 075b6fca-e4b5-4011-b54b-c17d58cdf908;0 57 + 11792 12143 99,99,99 1 351, 0, +chrM 11820 12134 7ce89482-16e1-483e-b5e0-b0134399bda2;0 49 + 11820 12134 99,99,99 1 314, 0, +chrM 11878 12130 6514b4ec-d4f5-4076-81e2-9046358db925;0 60 + 11878 12130 99,99,99 1 252, 0, +chrM 11896 12134 f0f29539-784d-42d2-9dad-eb25a26b49fb;0 8 + 11896 12134 99,99,99 1 238, 0, +chrM 12347 14332 f98c3bf4-1f39-4878-8f51-caf17de90899;0 60 + 12347 14332 99,99,99 1 1985, 0, +chrM 12348 14748 81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5;0 60 + 12348 14748 99,99,99 1 2400, 0, +chrM 12350 14747 edf3963d-76fb-4078-ac41-f8eb9f64e988;0 60 + 12350 14747 99,99,99 1 2397, 0, +chrM 12350 14163 deec63a9-179d-4c61-bd29-dafc6760477a;0 60 + 12350 14163 99,99,99 1 1813, 0, +chrM 12350 14748 cb422c65-69db-4a29-a9e8-e856a4f14683;0 60 + 12350 14748 99,99,99 1 2398, 0, +chrM 12351 14736 2004c78b-fea1-46fd-b496-2182a5d91c66;0 60 + 12351 14736 99,99,99 1 2385, 0, +chrM 12355 14741 d882ea6a-7ee2-4fd6-bd4f-12dd957e8dfc;0 60 + 12355 14741 99,99,99 1 2386, 0, +chrM 12359 14719 7a998ccc-f7ea-4596-bc3f-a03d26e4f9c8;0 60 + 12359 14719 99,99,99 1 2360, 0, +chrM 12360 14643 d543fc25-2ddd-41bf-bb6b-a4e74d426977;0 60 + 12360 14643 99,99,99 1 2283, 0, +chrM 12427 14577 643e91a1-9992-43e9-9f51-0d3c8ca2d5f0;0 60 + 12427 14577 99,99,99 1 2150, 0, +chrM 12740 13004 b9d88537-fc47-4868-8fd4-60793c6bf62f;0 60 + 12740 13004 99,99,99 1 264, 0, +chrM 12766 14747 68c26ba1-2760-4bb2-b641-5d89d8992391;0 60 + 12766 14747 99,99,99 1 1981, 0, +chrM 12816 13008 8831a73e-753b-4e63-a400-6a7cd0d69f20;0 60 + 12816 13008 99,99,99 1 192, 0, +chrM 13024 14744 14924af7-5502-4633-ae94-0bbd001ca21a;0 60 + 13024 14744 99,99,99 1 1720, 0, +chrM 13351 14735 7666594b-bf99-4138-aded-e47a4cec1a3f;0 43 + 13351 14735 99,99,99 1 1384, 0, +chrM 13431 14685 0f5e0bda-1534-498c-ac59-8d0e351dd995;0 60 + 13431 14685 99,99,99 1 1254, 0, +chrM 13517 14739 b7aaaaf0-1cb8-4a95-b428-502131fe5f71;0 60 + 13517 14739 99,99,99 1 1222, 0, +chrM 13607 14678 27d0e30a-e65c-423d-992b-5483d5565923;0 60 + 13607 14678 99,99,99 1 1071, 0, +chrM 13624 14538 b9308c6b-1169-48d8-a657-89ae33060235;0 60 + 13624 14538 99,99,99 1 914, 0, +chrM 13682 14507 59fea62b-afca-4ff2-860b-d993a0659919;0 60 + 13682 14507 99,99,99 1 825, 0, +chrM 13688 14674 3e7180dd-ea32-4deb-8129-d4f807e1efc8;0 60 + 13688 14674 99,99,99 1 986, 0, +chrM 14536 14748 78f8ac46-b6ce-4b75-b744-2276333f79ea;0 60 + 14536 14748 99,99,99 1 212, 0, +chrM 14541 14728 2e4d800c-7943-493e-8525-6caf58bbc02f;0 60 + 14541 14728 99,99,99 1 187, 0, +chrM 14552 14738 595b9542-db2b-47fc-aaa5-5fee9b7b3c16;0 60 + 14552 14738 99,99,99 1 186, 0, +chrM 14757 15887 22eceb47-b528-4c39-8254-0d60a604bd3f;0 60 + 14757 15887 99,99,99 1 1130, 0, +chrM 14757 15887 cf24a281-b665-4b8f-a3a3-528576c3067c;0 60 + 14757 15887 99,99,99 1 1130, 0, +chrM 14757 16045 fb76bcd3-041c-4e20-9175-ae434cbb3210;0 60 + 14757 16045 99,99,99 1 1288, 0, +chrM 14757 15670 f993603f-03f0-4fe4-9de0-4de82f7a0d0d;0 60 + 14757 15670 99,99,99 1 913, 0, +chrM 14757 15822 a6f7c93a-69a7-494b-a49a-eb8a64ce3918;0 60 + 14757 15822 99,99,99 1 1065, 0, +chrM 14757 15856 01c13ab7-ef27-4e62-ac39-638653276f7e;0 60 + 14757 15856 99,99,99 1 1099, 0, +chrM 14757 15869 5dac3f00-ff98-4945-944e-71670bc92587;0 60 + 14757 15869 99,99,99 1 1112, 0, +chrM 14758 15887 d69cbde2-2d60-4e19-ac83-817b0c69f28e;0 60 + 14758 15887 99,99,99 1 1129, 0, +chrM 14758 15886 016bc55b-7a52-4f24-b3d6-9132df099d80;0 60 + 14758 15886 99,99,99 1 1128, 0, +chrM 14758 15883 64e15f2e-0069-43b5-9dab-7940ef61c849;0 60 + 14758 15883 99,99,99 1 1125, 0, +chrM 14758 15887 6f6d8722-287e-4445-a9c8-94238428138f;0 60 + 14758 15887 99,99,99 1 1129, 0, +chrM 14758 15879 c072360c-3ac0-4097-8733-362a494a988e;0 60 + 14758 15879 99,99,99 1 1121, 0, +chrM 14760 15887 45bb9527-2be5-4272-b819-48a7971c6fbe;0 60 + 14760 15887 99,99,99 1 1127, 0, +chrM 14760 15883 7f6ec223-0a7f-415e-bdd8-0b2e2c4985ff;0 60 + 14760 15883 99,99,99 1 1123, 0, +chrM 14761 15847 95cb889c-4a97-4c29-a77c-3312a219a6ad;0 60 + 14761 15847 99,99,99 1 1086, 0, +chrM 14766 15887 f81dd59c-c08b-4c7d-8c23-1e47857afb92;0 60 + 14766 15887 99,99,99 1 1121, 0, +chrM 14766 15887 4a1cc098-aa5d-4ad9-87a6-fba57c10c7d7;0 60 + 14766 15887 99,99,99 1 1121, 0, +chrM 14770 15887 ce4659c3-382a-4361-b5ea-28c442883218;0 60 + 14770 15887 99,99,99 1 1117, 0, +chrM 14770 16075 90808752-db98-4215-b707-b0944c0a7272;0 60 + 14770 16075 99,99,99 1 1305, 0, +chrM 14778 14984 774ce748-fca6-4046-8daa-da7c6e91765a;0 60 + 14778 14984 99,99,99 1 206, 0, +chrM 14846 15115 76dc9f46-8b7b-48a8-9225-bca23777bda2;0 60 + 14846 15115 99,99,99 1 269, 0, +chrM 14924 15659 79eea848-d3ff-4e7b-9c01-9a3710c20732;0 60 + 14924 15659 99,99,99 1 735, 0, +chrM 14982 15842 dd484c35-375e-47a8-b9e8-31c0b4d39b4b;0 60 + 14982 15842 99,99,99 1 860, 0, +chrM 15009 15887 3bd3e3d3-132c-43e2-872a-8a41e25d8805;0 60 + 15009 15887 99,99,99 1 878, 0, +chrM 15169 15886 cdb71c09-5f6e-4145-99c6-3e0cbfd90739;0 60 + 15169 15886 99,99,99 1 717, 0, +chrM 15194 15883 2622775b-65c9-4cae-9a3b-c6be3e0faa17;0 60 + 15194 15883 99,99,99 1 689, 0, +chrM 15213 15876 3b1ef952-41fe-4d83-808c-76caa7f7b83d;0 60 + 15213 15876 99,99,99 1 663, 0, +chrM 15461 15887 9f0d3300-a9c3-41aa-af9b-00403ffbeacb;0 60 + 15461 15887 99,99,99 1 426, 0, +chrM 15496 15876 fbd51668-5fe6-431a-ad8b-fe1165eebf19;0 60 + 15496 15876 99,99,99 1 380, 0, +chrM 15587 15887 3c97e997-9eed-405b-b40e-28122064980c;0 60 + 15587 15887 99,99,99 1 300, 0, +chrM 15589 15887 32c06f69-94bc-4023-8ae7-f66dc584d355;0 30 + 15589 15887 99,99,99 1 298, 0, +chrM 15670 15874 4a827e6b-259e-4723-8860-f978ceaaa5f7;0 58 + 15670 15874 99,99,99 1 204, 0, +chrM 15695 15877 7e44209b-aae3-4993-91e4-fe5b37ab2eb2;0 55 + 15695 15877 99,99,99 1 182, 0, +chrM 15800 16569 a78fb847-612c-42c0-9b73-d59b91a9e9df;0 60 + 15800 16569 99,99,99 1 769, 0, +chrM 15963 16569 f6bd411a-d419-4197-a525-324568f7944a;0 60 + 15963 16569 99,99,99 1 606, 0, +chrM 15963 16540 ccdfb0ae-54fb-4e3d-8f92-587d4cdc7141;0 60 + 15963 16540 99,99,99 1 577, 0, +chrM 15968 16271 37432238-4f0a-4817-b648-73cb476a71d7;0 60 + 15968 16271 99,99,99 1 303, 0, +chrM 15970 16311 a446bc9e-f22d-40ca-a502-d78b06fc8dd4;0 60 + 15970 16311 99,99,99 1 341, 0, +chrM 15970 16557 2f14a1a9-c356-4568-9a4e-150c8d2038d0;0 60 + 15970 16557 99,99,99 1 587, 0, +chrM 15970 16296 19cc5328-7604-445f-b261-7e71a02273c6;0 60 + 15970 16296 99,99,99 1 326, 0, +chrM 15971 16569 46a0710f-c426-4f83-902b-a99be8273b34;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15971 16569 d52a572f-79ca-4109-a247-55ab7b0ceda6;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15972 16569 8bf3eb49-3aeb-4bc6-9bcc-1cfb1a896618;0 60 + 15972 16569 99,99,99 1 597, 0, +chrM 15976 16291 f051705e-4230-4631-84e3-7e014eb98f35;0 48 + 15976 16291 99,99,99 1 315, 0, diff -r 000000000000 -r 57dc46adf2da test-data/chrM.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,333 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT +TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG +GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC +CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA +AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT +GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT +TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT +ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC +CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA +ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA +GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT +AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA +ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC +ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT +AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC +GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA +GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT +CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC +TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC +CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG +AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC +AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA +GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG +GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC +TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC +AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA +GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA +CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA +ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT +TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG +AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT +GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA +CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT +CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC +CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA +AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT +AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA +GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA +ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG +TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA +TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC +AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA +CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA +GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcata +atcacttgttccttaaatagggacctgtatgaatggctccacgagggttc +agctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcg +ggcataacacagcaagacgagaagaccctatggagctttaatttaTTAAT +GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT +ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC +AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT +ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA +GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT +AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT +ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT +ATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccggt +aatcgcataaaacttaaaactttacagtcagaggttcaattcctcttctt +aacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT +CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC +AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC +TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG +CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC +AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC +AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG +CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC +ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT +TATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTC +GACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATA +CGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTA +TTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGAC +GCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACT +TCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCT +ACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCC +CCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTA +AATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaacc +catccctgagaatccaaaattctccgtgccacctatcacaccccatccta +AAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGG +TTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACT +CTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCT +AACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTCC +TCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAAC +AATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTC +ATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCT +TTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGC +CTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTAT +CCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAAA +ATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCT +ACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCC +TAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACC +CTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAAT +TCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATC +ATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCT +ACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACG +TAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCC +ACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACT +AATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGC +CCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAG +CCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCT +AAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAA +AAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAA +TTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGT +CTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCCA +CTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTC +TAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGT +AACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAAT +CTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAG +TTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAAC +ATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGC +TATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCC +TTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCAC +AACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCC +TCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTC +CCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAA +CACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAAC +ACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGA +ACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCC +TAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTA +GACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCAC +CGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGA +AATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACC +GTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAA +TAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTA +TTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTAT +CATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCC +TATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACA +TGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAAT +ATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCC +CCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaaa +aaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcc +tccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTC +AAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCG +CAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCAC +CTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATC +TCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCAT +CCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACG +AGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTAC +TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACAT +ACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTG +ACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAAC +AGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGAC +CGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGT +TTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGG +GCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGT +AAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACA +CCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATAT +TAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAA +AATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCA +TTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCT +ATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGAC +TAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATA +ACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCAT +TTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTA +TGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCT +AGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAG +TTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTA +CGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGG +AAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTA +ATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAA +CACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCC +ATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAG +CCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTA +ACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAG +CACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTC +TGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCA +CTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCC +TAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCAC +CATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTAT +TACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACT +TCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCT +CACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATC +ACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTT +TGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAG +TATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAA +AAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGCC +TTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCC +GCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTA +TTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAAC +AACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCC +TAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACC +GAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTA +TGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATA +TCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGC +TACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTA +TTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTA +CTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAA +CCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACT +GACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAAC +AACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCC +CCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCC +AACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCT +ATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGA +ACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGG +CTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACT +AATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTC +TCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTA +GCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTT +ATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTAC +TTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACA +CTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAG +ACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTA +GTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCAT +TCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAA +ACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGA +CTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCT +CGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGA +CTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAAC +ACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCA +CACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTA +TCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTT +AACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTA +TTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAG +GCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACAC +TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCA +CCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCC +ATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCAT +GTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCC +AAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACT +GTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTAC +TCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTC +CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT +CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA +TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA +TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG +GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA +GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC +AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC +TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA +GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC +CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA +CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA +TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT +CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT +TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA +CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT +ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA +ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA +TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC +ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA +CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT +TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC +TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT +CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC +CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC +TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT +CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC +ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA +TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC +ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA +TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA +ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT +AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG +GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC +AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA +CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC +ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC +ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG +CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC +ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA +TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC +CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG +AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG +CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC +TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT +GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG +AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT +CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG +ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC +AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC +TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG +CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC +CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC +AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT +ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT +AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG +ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG +ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT +ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC +CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA +CAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactC +CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA +CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA +ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC +CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT +CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT +TAAATAAGACATCACGATG diff -r 000000000000 -r 57dc46adf2da test-data/chrM.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa.fai Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,1 @@ +chrM 16569 6 50 51 diff -r 000000000000 -r 57dc46adf2da test-data/chrM.fastq.gz Binary file test-data/chrM.fastq.gz has changed diff -r 000000000000 -r 57dc46adf2da test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,1 @@ +chrM hg19 human mitochondrial genome ${__HERE__}/chrM.fa diff -r 000000000000 -r 57dc46adf2da test-data/flair.collapse.isoforms.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.bed Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,14 @@ +chrM 661 1341 ca7655f0-1077-4546-850f-be0f10f50a81_chrM:000 60 + 661 1341 14 1 680, 0, +chrM 1274 1601 07a2d20a-8f33-4283-87e2-ee2b28b771f2_chrM:1000 60 + 1274 1601 11 1 327, 0, +chrM 1681 3211 7739a708-0dd8-4e16-856c-0488b9378738_ENST00000387347.2 60 + 1681 3211 31 1 1530, 0, +chrM 3315 4220 13557349-20c1-42e2-8477-a31c29e524a3_ENST00000361390.2 60 + 3315 4220 58 1 905, 0, +chrM 4482 5439 7c64296d-12c2-49bd-a404-70478fff9a62_ENST00000361453.3 60 - 4482 5439 33 1 957, 0, +chrM 5591 5865 272f11a9-f8b7-4c23-8526-a36936b8527f_chrM:5000 29 + 5591 5865 66 1 274, 0, +chrM 5911 7518 1804a832-0ae7-4760-bd8c-2b8250455c48_ENST00000361624.2 60 + 5911 7518 167 1 1607, 0, +chrM 7596 8294 3065b2ed-affa-4e42-8c6e-b385487325f6_ENST00000361739.1 45 + 7596 8294 116 1 698, 0, +chrM 8377 9207 08c5eaa2-47a2-4813-ae6d-e579904d6416_ENST00000361899.2 42 + 8377 9207 77 1 830, 0, +chrM 9221 9991 29af7e32-7b11-4c36-ae11-25b54575faea_ENST00000362079.2 60 + 9221 9991 148 1 770, 0, +chrM 10070 10404 7258b7cf-cbd2-4dab-928d-bbb5bc115c4c_ENST00000361227.2 60 + 10070 10404 78 1 334, 0, +chrM 10482 12053 ccdaa81a-848a-4da0-abef-6411c5c3a01e_ENST00000361381.2 60 + 10482 12053 54 1 1571, 0, +chrM 12350 14748 81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5_ENST00000361567.2 60 + 12350 14748 20 1 2398, 0, +chrM 15971 16569 2f14a1a9-c356-4568-9a4e-150c8d2038d0_chrM:15000 60 + 15971 16569 3 1 598, 0, diff -r 000000000000 -r 57dc46adf2da test-data/flair.collapse.isoforms.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.fa Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,28 @@ +>ca7655f0-1077-4546-850f-be0f10f50a81_chrM:000 +TAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCC +>07a2d20a-8f33-4283-87e2-ee2b28b771f2_chrM:1000 +AAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAAC +>7739a708-0dd8-4e16-856c-0488b9378738_ENST00000387347.2 +CCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacctgtatgaatggctccacgagggttcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcgggcataacacagcaagacgagaagaccctatggagctttaatttaTTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACC +>13557349-20c1-42e2-8477-a31c29e524a3_ENST00000361390.2 +GCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTAGCATTACTTATATGATATGT +>7c64296d-12c2-49bd-a404-70478fff9a62_ENST00000361453.3 +GGGTGGGTTTTGTATGTTCAAACTGTCATTTTATTTTTACGTTGTTAGATATGGGGAGTAGTGTGATTGAGGTGGAGTAGATTAGGCGTAGGTAGAAGTAGAGGTTAAGGAGGGTGATGGTGGCTATGATGGTGGGGATGATGAGGCTATTGTTTTTTGTGAATTCTTCGATAATGGCCCATTTGGGCAAAAAGCCGGTTAGCGGGGGCAGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTTAGCTTGTTTCAGGTGCGAGATAGTAGTAGGGTCGTGGTGCTGGAGTTTAAGTTGAGTAGTAGGAATGCGGTAGTAGTTAGGATAATATAAATAGTTAAATTAAGAATGGTTATGTTAGGGTTGTACGGTAGAACTGCTATTATTCATCCTATGTGGGTAATTGAGGAGTATGCTAAGATTTTGCGTAGCTGGGTTTGGTTTAATCCACCTCAACTGCCTGCTATGATGGATAAGATTGAGAGAGTGAGGAGAAGGCTTACGTTTAGTGAGGGAGAGATTTGGTATATGATTGAGATGGGGGCTAGTTTTTGTCATGTGAGAAGAAGCAGGCCGGATGTCAGAGGGGTGCCTTGGGTAACCTCTGGGACTCAGAAGTGAAAGGGGGCTATTCCTAGTTTTATTGCTATAGCTATTATGATTATTAATGATGAGTATTGATTGGTAGTATTGGTTATGGTTCATTGTCCGGAGAGTATATTGTTGAAGAGGATAGCTATTAGAAGGATTATGGATGCGGTTGCTTGCGTGAGGAAATACTTGATGGCAGCTTCTGTGGAACGAGGGTTTATTTTTTTGGTTAGAACTGGAATAAAAGCTAGCATGTTTATTTCTAGGCCTACTCAGGTAAAAAATCAGTGCGAGCTTAGCGCTGTGATGAGTGTGCCTGCAAAGATGGTAGAGTAGATGACGGGTTGGG +>272f11a9-f8b7-4c23-8526-a36936b8527f_chrM:5000 +ACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGT +>1804a832-0ae7-4760-bd8c-2b8250455c48_ENST00000361624.2 +CGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaaaaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcctccatgactttttcAAAA +>3065b2ed-affa-4e42-8c6e-b385487325f6_ENST00000361739.1 +AGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCC +>08c5eaa2-47a2-4813-ae6d-e579904d6416_ENST00000361899.2 +AATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAA +>29af7e32-7b11-4c36-ae11-25b54575faea_ENST00000362079.2 +CATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTA +>7258b7cf-cbd2-4dab-928d-bbb5bc115c4c_ENST00000361227.2 +TTAATTTTAATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAAT +>ccdaa81a-848a-4da0-abef-6411c5c3a01e_ENST00000361381.2 +ACATAAATATTATACTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACAC +>81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5_ENST00000361567.2 +TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAAT +>2f14a1a9-c356-4568-9a4e-150c8d2038d0_chrM:15000 +TAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG diff -r 000000000000 -r 57dc46adf2da test-data/flair.collapse.isoforms.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair.collapse.isoforms.gtf Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,28 @@ +chrM FLAIR transcript 662 1341 . + . gene_id "chrM:000"; transcript_id "ca7655f0-1077-4546-850f-be0f10f50a81"; +chrM FLAIR exon 662 1341 . + 60 gene_id "chrM:000"; transcript_id "ca7655f0-1077-4546-850f-be0f10f50a81"; exon_number "0"; +chrM FLAIR transcript 1275 1601 . + . gene_id "chrM:1000"; transcript_id "07a2d20a-8f33-4283-87e2-ee2b28b771f2"; +chrM FLAIR exon 1275 1601 . + 60 gene_id "chrM:1000"; transcript_id "07a2d20a-8f33-4283-87e2-ee2b28b771f2"; exon_number "0"; +chrM FLAIR transcript 1682 3211 . + . gene_id "ENST00000387347.2"; transcript_id "7739a708-0dd8-4e16-856c-0488b9378738"; +chrM FLAIR exon 1682 3211 . + 60 gene_id "ENST00000387347.2"; transcript_id "7739a708-0dd8-4e16-856c-0488b9378738"; exon_number "0"; +chrM FLAIR transcript 3316 4220 . + . gene_id "ENST00000361390.2"; transcript_id "13557349-20c1-42e2-8477-a31c29e524a3"; +chrM FLAIR exon 3316 4220 . + 60 gene_id "ENST00000361390.2"; transcript_id "13557349-20c1-42e2-8477-a31c29e524a3"; exon_number "0"; +chrM FLAIR transcript 4483 5439 . - . gene_id "ENST00000361453.3"; transcript_id "7c64296d-12c2-49bd-a404-70478fff9a62"; +chrM FLAIR exon 4483 5439 . - 60 gene_id "ENST00000361453.3"; transcript_id "7c64296d-12c2-49bd-a404-70478fff9a62"; exon_number "0"; +chrM FLAIR transcript 5592 5865 . + . gene_id "chrM:5000"; transcript_id "272f11a9-f8b7-4c23-8526-a36936b8527f"; +chrM FLAIR exon 5592 5865 . + 29 gene_id "chrM:5000"; transcript_id "272f11a9-f8b7-4c23-8526-a36936b8527f"; exon_number "0"; +chrM FLAIR transcript 5912 7518 . + . gene_id "ENST00000361624.2"; transcript_id "1804a832-0ae7-4760-bd8c-2b8250455c48"; +chrM FLAIR exon 5912 7518 . + 60 gene_id "ENST00000361624.2"; transcript_id "1804a832-0ae7-4760-bd8c-2b8250455c48"; exon_number "0"; +chrM FLAIR transcript 7597 8294 . + . gene_id "ENST00000361739.1"; transcript_id "3065b2ed-affa-4e42-8c6e-b385487325f6"; +chrM FLAIR exon 7597 8294 . + 45 gene_id "ENST00000361739.1"; transcript_id "3065b2ed-affa-4e42-8c6e-b385487325f6"; exon_number "0"; +chrM FLAIR transcript 8378 9207 . + . gene_id "ENST00000361899.2"; transcript_id "08c5eaa2-47a2-4813-ae6d-e579904d6416"; +chrM FLAIR exon 8378 9207 . + 42 gene_id "ENST00000361899.2"; transcript_id "08c5eaa2-47a2-4813-ae6d-e579904d6416"; exon_number "0"; +chrM FLAIR transcript 9222 9991 . + . gene_id "ENST00000362079.2"; transcript_id "29af7e32-7b11-4c36-ae11-25b54575faea"; +chrM FLAIR exon 9222 9991 . + 60 gene_id "ENST00000362079.2"; transcript_id "29af7e32-7b11-4c36-ae11-25b54575faea"; exon_number "0"; +chrM FLAIR transcript 10071 10404 . + . gene_id "ENST00000361227.2"; transcript_id "7258b7cf-cbd2-4dab-928d-bbb5bc115c4c"; +chrM FLAIR exon 10071 10404 . + 60 gene_id "ENST00000361227.2"; transcript_id "7258b7cf-cbd2-4dab-928d-bbb5bc115c4c"; exon_number "0"; +chrM FLAIR transcript 10483 12053 . + . gene_id "ENST00000361381.2"; transcript_id "ccdaa81a-848a-4da0-abef-6411c5c3a01e"; +chrM FLAIR exon 10483 12053 . + 60 gene_id "ENST00000361381.2"; transcript_id "ccdaa81a-848a-4da0-abef-6411c5c3a01e"; exon_number "0"; +chrM FLAIR transcript 12351 14748 . + . gene_id "ENST00000361567.2"; transcript_id "81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5"; +chrM FLAIR exon 12351 14748 . + 60 gene_id "ENST00000361567.2"; transcript_id "81c2d0d9-44c7-4f0a-bb58-7b0ab49220a5"; exon_number "0"; +chrM FLAIR transcript 15972 16569 . + . gene_id "chrM:15000"; transcript_id "2f14a1a9-c356-4568-9a4e-150c8d2038d0"; +chrM FLAIR exon 15972 16569 . + 60 gene_id "chrM:15000"; transcript_id "2f14a1a9-c356-4568-9a4e-150c8d2038d0"; exon_number "0"; diff -r 000000000000 -r 57dc46adf2da test-data/flair_all_corrected.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair_all_corrected.bed Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,1340 @@ +chrM 569 1461 1fb96112-b5ee-46ac-9ca4-c3e170512e4d;0 60 + 569 1461 99,99,99 1 892, 0, +chrM 570 1631 ca7655f0-1077-4546-850f-be0f10f50a81;0 60 + 570 1631 99,99,99 1 1061, 0, +chrM 570 3149 07a2d20a-8f33-4283-87e2-ee2b28b771f2;0 60 + 570 3149 99,99,99 1 2579, 0, +chrM 571 1180 fd4b26fc-72f9-4060-8c6d-deca2e55cceb;0 60 + 571 1180 99,99,99 1 609, 0, +chrM 571 1041 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99,99,99 1 206, 0, +chrM 14846 15115 76dc9f46-8b7b-48a8-9225-bca23777bda2;0 60 + 14846 15115 99,99,99 1 269, 0, +chrM 14924 15659 79eea848-d3ff-4e7b-9c01-9a3710c20732;0 60 + 14924 15659 99,99,99 1 735, 0, +chrM 14982 15842 dd484c35-375e-47a8-b9e8-31c0b4d39b4b;0 60 + 14982 15842 99,99,99 1 860, 0, +chrM 15009 15887 3bd3e3d3-132c-43e2-872a-8a41e25d8805;0 60 + 15009 15887 99,99,99 1 878, 0, +chrM 15169 15886 cdb71c09-5f6e-4145-99c6-3e0cbfd90739;0 60 + 15169 15886 99,99,99 1 717, 0, +chrM 15194 15883 2622775b-65c9-4cae-9a3b-c6be3e0faa17;0 60 + 15194 15883 99,99,99 1 689, 0, +chrM 15213 15876 3b1ef952-41fe-4d83-808c-76caa7f7b83d;0 60 + 15213 15876 99,99,99 1 663, 0, +chrM 15461 15887 9f0d3300-a9c3-41aa-af9b-00403ffbeacb;0 60 + 15461 15887 99,99,99 1 426, 0, +chrM 15496 15876 fbd51668-5fe6-431a-ad8b-fe1165eebf19;0 60 + 15496 15876 99,99,99 1 380, 0, +chrM 15587 15887 3c97e997-9eed-405b-b40e-28122064980c;0 60 + 15587 15887 99,99,99 1 300, 0, +chrM 15589 15887 32c06f69-94bc-4023-8ae7-f66dc584d355;0 30 + 15589 15887 99,99,99 1 298, 0, +chrM 15670 15874 4a827e6b-259e-4723-8860-f978ceaaa5f7;0 58 + 15670 15874 99,99,99 1 204, 0, +chrM 15695 15877 7e44209b-aae3-4993-91e4-fe5b37ab2eb2;0 55 + 15695 15877 99,99,99 1 182, 0, +chrM 15800 16569 a78fb847-612c-42c0-9b73-d59b91a9e9df;0 60 + 15800 16569 99,99,99 1 769, 0, +chrM 15963 16569 f6bd411a-d419-4197-a525-324568f7944a;0 60 + 15963 16569 99,99,99 1 606, 0, +chrM 15963 16540 ccdfb0ae-54fb-4e3d-8f92-587d4cdc7141;0 60 + 15963 16540 99,99,99 1 577, 0, +chrM 15968 16271 37432238-4f0a-4817-b648-73cb476a71d7;0 60 + 15968 16271 99,99,99 1 303, 0, +chrM 15970 16311 a446bc9e-f22d-40ca-a502-d78b06fc8dd4;0 60 + 15970 16311 99,99,99 1 341, 0, +chrM 15970 16557 2f14a1a9-c356-4568-9a4e-150c8d2038d0;0 60 + 15970 16557 99,99,99 1 587, 0, +chrM 15970 16296 19cc5328-7604-445f-b261-7e71a02273c6;0 60 + 15970 16296 99,99,99 1 326, 0, +chrM 15971 16569 46a0710f-c426-4f83-902b-a99be8273b34;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15971 16569 d52a572f-79ca-4109-a247-55ab7b0ceda6;0 60 + 15971 16569 99,99,99 1 598, 0, +chrM 15972 16569 8bf3eb49-3aeb-4bc6-9bcc-1cfb1a896618;0 60 + 15972 16569 99,99,99 1 597, 0, +chrM 15976 16291 f051705e-4230-4631-84e3-7e014eb98f35;0 48 + 15976 16291 99,99,99 1 315, 0, diff -r 000000000000 -r 57dc46adf2da test-data/flair_all_inconsistent.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flair_all_inconsistent.bed Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,8 @@ +chrM 1692 16233 8e95941f-3681-40f9-98c2-f5dee4c29acd;0 60 + 1692 16233 27,158,119 2 881,20, 0,14521, +chrM 2011 10881 4d2c4cb6-5652-4bff-aeaa-1a7501b9203e;0 60 + 2011 10881 99,99,99 2 1237,30, 0,8840, +chrM 3258 4226 a6aa00e3-7d42-431e-aa9b-f974416c184b;0 60 - 3258 4226 217,95,2 2 563,338, 0,630, +chrM 3328 4257 c2a3dfdd-b7b9-4af8-b933-d7042384d0cc;0 60 - 3328 4257 217,95,2 2 187,628, 0,301, +chrM 4482 9899 d49d098d-20e2-471c-b621-aea607dcf717;0 58 - 4482 9899 217,95,2 2 1016,46, 0,5371, +chrM 4737 8145 8c9e8a40-b47d-43f7-bc54-d15976e27c0c;0 60 - 4737 8145 217,95,2 2 725,15, 0,3393, +chrM 5911 12712 78cc6deb-e14a-479f-a24e-7941deded72c;0 60 + 5911 12712 27,158,119 2 1609,72, 0,6729, +chrM 11384 12143 af53d265-544a-420b-ae7b-8b56aebe1ac7;0 60 - 11384 12143 217,95,2 2 65,642, 0,117, diff -r 000000000000 -r 57dc46adf2da tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff -r 000000000000 -r 57dc46adf2da tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r 57dc46adf2da tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Nov 27 21:56:08 2020 +0000 @@ -0,0 +1,6 @@ + + + value, dbkey, name, path + +
+