Merge branch 'feature-ag/new-germlines' into 'dev'

Update germlines

See merge request !247

algo/tests/should-get-tests/10-md5-germline.should-get

@@ -3,25 +3,25 @@
 
 $ Check md5 in germline/, sequences split and processed from germline and other databases
 1:b64be21f03b290c6850ce2cb2f1d6f02 homo-sapiens/IGHD.fa
-1:f38ca03b7672641c7b3c0e7787311bb8 homo-sapiens/IGHJ.fa
-1:e4da5f60a89df3879538bf00d9e7f5c9 homo-sapiens/IGHV.fa
+1:6a64f90ea2d19721d410c545e9d0bb9e homo-sapiens/IGHJ.fa
+1:73e6adab4faeb48b4fc2904e3a6e90f8 homo-sapiens/IGHV.fa
 1:0367825e404f753f0890b8f52aec7502 homo-sapiens/IGKJ.fa
-1:10ffddf98d73396b46c521c6999bbd09 homo-sapiens/IGKV.fa
+1:820188b335764f0eb04578ea35bbb143 homo-sapiens/IGKV.fa
 1:af257e110cf1ec6c38457af82a8118aa homo-sapiens/IGLJ.fa
-1:721f5afdf6ea9af5bafad4226d7e7f15 homo-sapiens/IGLV.fa
-1:bf915f443a26733f82391baae221c0d4 homo-sapiens/TRAJ.fa
-1:26013bcd4988623da89900646ce94387 homo-sapiens/TRAV.fa
+1:d6fa96cbc4de984729154c9d2217e3d2 homo-sapiens/IGLV.fa
+1:f0c43d7b0074e155aef411ea7353c23e homo-sapiens/TRAJ.fa
+1:935d588445e94d575c412cb3699b6bff homo-sapiens/TRAV.fa
 1:5b74170b9c45b9243558941bf07666ff homo-sapiens/TRBD.fa
 1:b9f8390d1d18a9ef5db9ab6875e196f1 homo-sapiens/TRBJ.fa
-1:b27a826a947b2fe17c82799753773538 homo-sapiens/TRBV.fa
+1:6540dc6a0e4f84de208a8b1f5d9fa981 homo-sapiens/TRBV.fa
 1:7f9fe8eaf781cf87453c157a771d5aaf homo-sapiens/TRDD.fa
 1:e50fc3c2f786f0b5a2b6fb5834dd3814 homo-sapiens/TRDJ.fa
-1:1dbb96884c9d479af59e216d4a9f7143 homo-sapiens/TRDV.fa
-1:4f6495933de0b93cfcc2e4ac00d1ecaa homo-sapiens/TRGJ.fa
-1:6094243f35263dfcc96e75adbfe8c04b homo-sapiens/TRGV.fa
+1:36dbb85d696634b8ee6ba0dc7500af85 homo-sapiens/TRDV.fa
+1:552cbc4883f3524fdc871fc156ecfdde homo-sapiens/TRGJ.fa
+1:e50df5cf337648190bc59609fe5fb5e0 homo-sapiens/TRGV.fa
 1:6f585362d727b243dd284ede15118670 mus-musculus/IGHD.fa
 1:218632e3e3c4fcd4c9ca7281e8976e3a mus-musculus/IGHJ.fa
-1:5cdc40857ff3084ed2d7163706b11f1d mus-musculus/IGHV.fa
+1:d389ee1e204699942ec1185fad8cd3df mus-musculus/IGHV.fa
 1:47568ad1ee648410b734c3b33f4a9eea mus-musculus/IGKJ.fa
 1:e2774dbad5e73f3b0c1e46aeab285baa mus-musculus/IGKV.fa
 1:750276a78c3b55f378449ecdcb9c3f78 mus-musculus/IGLJ.fa
@@ -38,14 +38,14 @@ $ Check md5 in germline/, sequences split and processed from germline and other
 1:982c0fc1208d066bc028621e94d2b466 mus-musculus/TRGV.fa
 1:d55f4acf266d3bae4a7f9b3aa1881abc rattus-norvegicus/IGHD.fa
 1:07fa1dbe7a70f34c9a4e42ba9e9d7ca1 rattus-norvegicus/IGHJ.fa
-1:f5382906485e36c05fb6cbd877eb2896 rattus-norvegicus/IGHV.fa
+1:877b03603ec7e2a99d10184c3636f635 rattus-norvegicus/IGHV.fa
 1:c5ca90bea438f929308c5d57dfb1dc6b rattus-norvegicus/IGKV.fa
 1:96bc9d75e6b072e5d643c195ed562497 rattus-norvegicus/IGLJ.fa
 1:7e5c54685597270f333b41b70aef74ad rattus-norvegicus/IGLV.fa
 
 $ Check md5 in germline/, other sequences
+1:957b46da4114a1ed66f2e9b5d06aff2a homo-sapiens/CD.fa
 1:9112d6975669ccb59970fa79ceef599d homo-sapiens/CD-sorting.fa
-1:e6540659d36fa37f83f7e1463dde906f homo-sapiens/CD.fa
 1:eb32e780af5a4b8c0d1e9d780bacac43 homo-sapiens/IGHC=A1.fa
 1:b1ea36c4255c63d775ecdb03967ec89e homo-sapiens/IGHC=A2.fa
 1:43c54f3ddedfde87f70b0e0bea2d6d5f homo-sapiens/IGHC=D.fa
@@ -56,20 +56,20 @@ $ Check md5 in germline/, other sequences
 1:d5123a856e2dedacfcfcd5fd11ebc2bc homo-sapiens/IGHC=G4.fa
 1:6c1e3e61d5824a03f71a5527ccdbb35c homo-sapiens/IGHC=GP.fa
 1:dd2263230c64abb9a22f5f8b7a979275 homo-sapiens/IGHC=M.fa
-1:2ed67cdd3d8f8fe3096afe747a0df205 homo-sapiens/IGHD.up.fa
-1:a13a4c31570952c6c7fc1e7161051675 homo-sapiens/IGHJ.down.fa
+1:cbf6cde7e7391c58229f815034cfbfa3 homo-sapiens/IGHD.up.fa
+1:3fb492cfdbd9f9e640d15e457f7af82f homo-sapiens/IGHJ.down.fa
 1:7d6247262807ad5478b7a4e52a59c568 homo-sapiens/IGK-INTRON.fa
+1:17d62684cad533025a25401cf7974d50 homo-sapiens/IGKJ.down.fa
 1:1147a04c4e8a8dd534aae65db1ae13ca homo-sapiens/IGK-KDE.fa
-1:805f326b92db78d8276b5a58b0f93fa2 homo-sapiens/IGKJ.down.fa
-1:9f37008bdabf1d7102d753845e36309e homo-sapiens/IGLJ.down.fa
-1:68e06198c4f41898533fecd30b86a446 homo-sapiens/TRAJ.down.fa
-1:79f9526d456d4550c1451a67e34efa51 homo-sapiens/TRBD.up.fa
-1:052da0d01539810a3ede514ade7ec988 homo-sapiens/TRBJ.down.fa
-1:e0a1860c5f9f937800c4b9d090f0c8aa homo-sapiens/TRDD.up.fa
-1:4f1d8f0e508e7e40adbd8896b64a905c homo-sapiens/TRDD2.up.fa
-1:d8017c8ee68383b874f7ff00efab0db6 homo-sapiens/TRDD3.down.fa
-1:a0a77c861cb4abc5222fad9da143e2b9 homo-sapiens/TRDJ.down.fa
-1:f1ae8b4f91c3ab3cad31e490f09eeff0 homo-sapiens/TRGJ.down.fa
+1:c7ff31249a38e29429f5e6144123274a homo-sapiens/IGLJ.down.fa
+1:25fb374147fdf5e73242b7776d9d73e2 homo-sapiens/TRAJ.down.fa
+1:86ff6637be816b145fd69153d84bbcf1 homo-sapiens/TRBD.up.fa
+1:a6cf4d4ea828cabba9061fa794662fff homo-sapiens/TRBJ.down.fa
+1:ff05546d9fa09c81c82914c8af19c3a0 homo-sapiens/TRDD2.up.fa
+1:7104ce2e1fc0461d475026c2a560947b homo-sapiens/TRDD3.down.fa
+1:fa8fce50396e96bb7eed892f68717957 homo-sapiens/TRDD.up.fa
+1:ee091b204ffdcf2b29b60d7c4435abe5 homo-sapiens/TRDJ.down.fa
+1:bec6c2dfa3c4535b87a89f9ade4a25e0 homo-sapiens/TRGJ.down.fa
 1:48f54c5af4f8d748ab2f02b2a6ea3370 mus-musculus/IGHC=A.fa
 1:25cb0451d31ca5337d462eb648914fe7 mus-musculus/IGHC=D.fa
 1:8f2ec40bc77a4e7f0c7b19655812ddbc mus-musculus/IGHC=E.fa
@@ -79,25 +79,25 @@ $ Check md5 in germline/, other sequences
 1:03cd9b5729ec3de23b302c476a51c9d3 mus-musculus/IGHC=G2C.fa
 1:744e59a4b5d1fc53beae91a0bee8f34a mus-musculus/IGHC=G3.fa
 1:b72bc2ed53226dd68519bb0cb679f608 mus-musculus/IGHC=M.fa
-1:bacb56a07cfcd93a4734fa25a832a805 mus-musculus/IGHD.up.fa
-1:07cd7e934d5ad5b804b5e8008c3f6662 mus-musculus/IGHJ.down.fa
-1:94cb5eaa7f9b1732fe9f21bfaee11af7 mus-musculus/IGKJ.down.fa
-1:8b2a0ea8303c8bc21ca6c9669a91cc7a mus-musculus/IGLJ.down.fa
-1:f3840f00f202cafd36d2cd3b17608bbd mus-musculus/TRAJ.down.fa
-1:60ad210f435d4f31b37f0254bf9d96fe mus-musculus/TRBD.up.fa
-1:8be584820144e5f8960ac71361752f10 mus-musculus/TRBJ.down.fa
-1:97a0118ff5659b8e46e937e3b4afa43c mus-musculus/TRDD.up.fa
-1:b1e00c7630580fd3c79801ae9174734d mus-musculus/TRDD2.up.fa
-1:5481f5e78573695406baa58a04689d2c mus-musculus/TRDJ.down.fa
-1:1d823716238ad85afe903fa7db8604c2 mus-musculus/TRGJ.down.fa
+1:123ebf4aaaa3b530c1911c0febcd74a5 mus-musculus/IGHD.up.fa
+1:8353980dac74af8bffe3de0b746a897e mus-musculus/IGHJ.down.fa
+1:f6282c17fb689899d37627df79194b38 mus-musculus/IGKJ.down.fa
+1:9716ccba4912b32c462cad5c0cd82bed mus-musculus/IGLJ.down.fa
+1:d3e2887e41fac79c6287c630050dcffe mus-musculus/TRAJ.down.fa
+1:89bcd757dfd42615307d9970307f6e01 mus-musculus/TRBD.up.fa
+1:29d23ea1a84881b21bcf38cd004b94e3 mus-musculus/TRBJ.down.fa
+1:a3dd73f39e659c3008d3f595c7731792 mus-musculus/TRDD2.up.fa
+1:ffa36242abfedd81c563ddf74a8d304a mus-musculus/TRDD.up.fa
+1:c709bb05205022b0aefad45b4eb72169 mus-musculus/TRDJ.down.fa
+1:a234e3568f9553eef28799b8d5189d81 mus-musculus/TRGJ.down.fa
 1:90075c7d51bd1d08892163848a8f2ecc rattus-norvegicus/IGHC=A.fa
-1:e0d2d3e90980bf783e35d3775a3c327d rattus-norvegicus/IGHC=D.fa
+1:6cf27ae32f98ec8f912e0d07b46a2139 rattus-norvegicus/IGHC=D.fa
 1:8461bb440ad2264eb638d948bda186ab rattus-norvegicus/IGHC=E.fa
 1:72537faac0e87d1265c7806c300a41ce rattus-norvegicus/IGHC=G1.fa
 1:4234f1b5e763f51782c88358e2085714 rattus-norvegicus/IGHC=G2A.fa
 1:6f2605929ae226fd7ebaf9b40d948a85 rattus-norvegicus/IGHC=G2B.fa
 1:36f7704ea32dbc0eb71c4ffbe459c23c rattus-norvegicus/IGHC=G2C.fa
 1:a27b6fc827063a041062a8b4b2945232 rattus-norvegicus/IGHC=M.fa
-1:a122818ff4b6ef5e2013a1ae1c493425 rattus-norvegicus/IGHD.up.fa
+1:84362ee627d5e3d78579aedc18ba6aef rattus-norvegicus/IGHD.up.fa
 1:3445516778ab4fbf96cf4008a40e6fe2 rattus-norvegicus/IGHJ.down.fa
-1:69aa6db3bb8a332289ab3b5cf5ab3b5a rattus-norvegicus/IGLJ.down.fa
+1:50d821031cee5e1a3849966fafdc2ad5 rattus-norvegicus/IGLJ.down.fa

algo/tests/should-get-tests/stanford-Z.should-get

@@ -6,4 +6,4 @@ $ Clone 13 is correctly analyzed
 
 $ Statistics on -Z
 1:Statistics on clone analysis
-rb1: IGH 1579/ 10470 15..%
+rb1: IGH 1[5-7][0-9]{2}/ 1[0-2][0-9]{3} 15..%

algo/tests/should-get-tests/stanford-germlines.should-get

@@ -4,7 +4,7 @@ $ number of reads and kmers
 1:13153 reads, 3020179 kmers
 
 $ k-mers, IGHV
-1:13115 .* 1222841 .*IGHV
+1:13115 .* 1222984 .*IGHV
 
 $ k-mers, IGHJ
 1:38 .* 435867 .*IGHJ
@@ -13,5 +13,5 @@ $ k-mers, ambiguous
 1:47648   .*\\?
 
 $ k-mers, unknown
-1:1251709 .*_
+1:1251567 .*_
 

algo/tests/should-get-tests/stanford-w100.should-get

@@ -7,10 +7,10 @@ $ Find the good number of "too short sequences" for windows of size 100
 1: UNSEG too short w ->      0
 
 $ Some reads have shortened or shifted windows
-1: SEG changed w -> 1368
+1: SEG changed w -> 1369
 
 $ Most changed windows are just shifted
-913: w100/-5
+914: w100/-5
 360: w100/-10
 
 $ Some changed windows are lighlty shortened
@@ -24,7 +24,7 @@ $ Find the good number of windows in Stanford S22
 1: found 11835 windows in 13152 reads
 
 $ Find the correct number of clones with shifted of shortened windows
-1243: "Short or shifted window"
-1243: "W50"
+1244: "Short or shifted window"
+1244: "W50"
 
 

algo/tests/should-get-tests/stanford.should-get

@@ -5,7 +5,7 @@ $ Germlines are custom
 1: custom germlines
 
 $ Parses IGHV.fa germline
-1: 101925 bp in 349 sequences
+1: 104369 bp in 357 sequences
 
 $ Parses IGHD.fa germline
 1: 1070 bp in  44 sequences

algo/tests/should-vdj-tests/0000-nck-TRB+.should-vdj.fa

->TRBD2*02 8/10/2 TRBJ2-7*01  [TRB+]
+# TRBD2*01                                               GCAGGGAGGAAACATTTTTGTATCATGGTGTAACATTGTGGGGACTAGCGGGGGGG
+#                                                        ||||||||||||||||||||||||||||||||||||||||||||||||
+# read        CTGCGCTTCCTGCCGCTGCCcaGTGGTTGGGGGAGGGGGACtaGCAGGGAGGAAACATTTTTGTATcaTGGTGTAACATTGTGGGGACTAGTGTCAGTCCCCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTTACAGGTAAG
+#                                                        ||||||||||||||||||||||||||||||||||||||||||||||||
+# TRBD2*02                                               GCAGGGAGGAAACATTTTTGTATCATGGTGTAACATTGTGGGGACTAGCGGGAGGG
+
+>TRBD2 8/10/2 TRBJ2-7*01  [TRB+]
 CTGCGCTTCCTGCCGCTGCCcaGTGGTTGGGGGAGGGGGACtaGCAGGGAGGAAACATTTTTGTATcaTGGTGTAACATTGTGGGGACTAGTGTCAGTCCCCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTTACAGGTAAGA
 >TRBD2*02 3/9/7 TRBJ2-1*01  [TRB+]
 CTGCGCTTCCTGCCGCTGCCcaGTGGTTggggGAGGGGGACtaGCAGGGAGGAAACATTTTTGTATATGGTGTAACATTGTGGGGACTAGCGGGAAGTAGGAGGAATGAgCAGTTCTTCGGGCCAGGGACACGGCTCACCGTGCTAGGTAAGAAGG

algo/tests/should-vdj-tests/0119-lil-IGK+-TRA+D-TRD+-TRG.should-vdj.fa

@@ -9,7 +9,7 @@ CGTGGCACCGCGAGCTGTAGACAGAGCCGCGGTCTTTCTCGATTGAGTGGCTTTGGTGGCCATGCCACCGCGCTCTTGGG
 >IGKV3-7*04 1/GTGGA/11 KDE  [IGK+] 
 CCCAGGCTCCTCATCTATGATGCATCCACCAGGGCCACTAGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGGATTATAACTTACCTCGTGGAGGCAGCCCAGGGCGACTCCTCATGAGTCTGCAGCTGCATTTTTGCCATATCCACTATTTGGAGTCTGACCTCCCTAGGAAGCCTCCCTGCTCCCTAGGACAACCTGCTCTGACCTCTGAGG
 
->TRGV2*01 9/CCCTGG/1 TRGJP1*01  [TRG]  {CATPW!TTGWFKIF}
+>TRGV2*03 9/CCCTGG/1 TRGJP1*01  [TRG]  {CATPW!TTGWFKIF}
 GGAAGGCCCCACAGCGTCTTCAGTACTATGACTCCTACAACTCCAAGGTTGTGTTGGAATCAGGAGTCAGTCCAGGGAAGTATTATACTTACGCAAGCACAAGGAACAACTTGAGATTGATACTGCGAAATCTAATTGAAAATGACTTTGGGGTCTATTACTGTGCCACCCCCTGGTACCACTGGTTGGTTCAAGATATTTGCTGAAGGGACTAAGCTCATAGTAACTTCGCCTGGTAA
 
 # or TRGJ1*01

algo/tests/should-vdj-tests/BRI_multi.should-vdj.fa

@@ -11,7 +11,7 @@ TTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGTAAG
 
 
 # target 1297RC
->IGHV2-70D*04 4/TCCCG/10 IGHD3-10*01 10/CCTTG/0  IGHJ5*02 [IGH]
+>(IGHV2-70D*04, IGHV2-70*04) 4/TCCCG/10 IGHD3-10*01 10/CCTTG/0  IGHJ5*02 [IGH]
 gacctgcaccttctctgggttctcactcagcactagtggaatgcgtgcgagctggatccgtcagcccccagg
 gaaggccctggagtggcttgcacgcattgattgggatgatgataaattctacagcacatctctgaagaccag
 gctcaccatctccaaggacacctccaaaaaccaggtggtccttacaatgaccaacatggaccctgtggacac

algo/tests/should-vdj-tests/gosh-igh.should-vdj.fa

@@ -35,7 +35,7 @@ GGCTTATCCTTCGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGGAAGGGACTGGAATAGTGTTTCAGCTATTAG
 CGGGGTAGGTCTCTGCAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGATAAGGCCAGTATTATCCCGTGGAGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTA
 
 #1465 vh6
->IGHV6-1*01 4/14/1 IGHD2-2*01 7/8/6 IGHJ6*02  [IGH]
+>IGHV6-1*01 4/14/1 (IGHD2-2*01, IGHD2-2*02) 7/8/6 IGHJ6*02  [IGH]
 CTCCTGTGCATCTCCGGGGACAGTGTCTCTAGCAACAGTGCTGCTTGGAACTGGATCAGGCAGTCCCCATCGAGAGGCCTTGAGTGGCTGGGAAGGACATACTACAGGTCCAAGTGGTATAATGATTATGCAGTATCTGTGAAAAGTCGAATAACCATCAACCCAGACACATCCAAGAACCAGTTCTCCCTGCAGCTGAACTCTGTGACTCCCGAGGACACGGCTGTGTATTACTGTGCAACGGGGGGTTCTGCGGGATATTGTAGTAGTACCAGCTGTCCCTCGGACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGT
 
 #1465 dh3
@@ -80,11 +80,11 @@ GCTGGCAGATTCTGCAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGG
 CGGGGTAGTCTCCTGCAGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGGGGGGCTGGAACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAAACTTATCCTTGGAAAGACGTCATCCGTAGTAGTAGTTCAGCCCCCCTGCCGTAATACAGGCCGTGTCTCGATCTCAGCGGCTCACTCCTGGTGGGCTGTGCTTGTGGAATTCTCCCGGTAATCGTGACTTTGCCCTGGAAATTCTATGCCTATTGTTGCTGGACC
 
 #1428 vh2
->IGHV2-70*04 IGHJ6*02  [IGH] BUG
+>(IGHV2-70*04  IGHJ6*02, IGHV2-70D*04  IGHJ6*02)  [IGH]
 CCACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGTTGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAAACCACGTCCTTGGCCCGACTCCATACCACACCTAATACCTGGCTGTGTCCACGAGGATCCATGGTTGGGCATTGTAGGACCACTGGTTTTTGGAAGTTCCCTTGAGAAAAGAAAAACAGAATCTTCAAAAAA
 
 #1428 vh3
->(IGHV3-30*18, IGHV3-30-5*01) IGHD3-22*01 IGHJ2*01  [IGH]
+>(IGHV3-30*18 IGHD3-22*01 IGHJ2*01, IGHV3-30-5*01 IGHD3-22*01 IGHJ2*01)  [IGH]
 CGCCATGATCTTCGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAACCGAGACCCTAATTCCTTTTATTACTATGATAGTAGTGGTTATTTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACCGTCTCCTCAGGTCAAACCAGGTGCAGGCGCATGATCGAAGTACAAATAACACTACTATCAAAGTAATAAAAGGGAATTATGGGTTCGGTTCCACGTTA
 
 #1428 vh4
@@ -100,7 +100,7 @@ TAGTCTCCTGCAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGSACAAGGGCTTG
 GTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGCAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGGGATAAAACGGTATAGCAGCAGCTGGGGGAGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGTA
 
 #1416 dh5
->IGHD5-18*01 5/12/15 IGHJ6*03  [IGH+] BUG
+>(IGHD5-18*01, IGHD5-5*01) 5/12/15 IGHJ6*03  [IGH+]
 ACCCCMTGTCCAGTCCTGGGGGCCCCTGGCACAGCTGTCTGGACCCTCTCTATTCCCTGGGAAGCTCCYCCTGACAGCCCCGCCTCCAGTTCCAGGTGTGGTTATTGTCAGGGGGTGTCAGACTGTGGTGGATACAGCTATGACCCCCCCAAAGACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGG
 
 #1411 vh1
@@ -156,7 +156,7 @@ AGCTCTGCTGATTTGTGGGCACTTATGAACCCGAAAGGACATGGCCATGGGGTGGGTAGGGACATAGGGACAGATGCCAG
 CGCCCCACTTGATATTCCTTTTAGCCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGGGTGGGAGGTATTAAACTATGGTTCGGGGAGTTATTATAACGTTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCCTCAGGTAACTC
 
 #1347 vh2
->IGHV2-26*01 0/5/5 IGHD5-24*01 4/13/7 IGHJ4*02  [IGH]
+>IGHV2-26*02 0/5/5 IGHD5-24*01 4/13/7 IGHJ4*02  [IGH] BUG-LOCUS
 TCAGAGACCTCACGCTGACCTGCACCGTCTCTGGGTTCTCACTCAGCAATGCTAGAATGGGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACACATTTTTTCGAATGACAAAAAATCCTACAGCACATCTCTGAAGAGCAGGCTCACCATCTCCAAGGACACCTCCAAAAGCCAGGTGGTCCTTACCATGACCAATATGGACCCTGTGGACACAGCCACATATTACTGTGCATGGATACCCGAGGATGGCTACAACGACAAGAGCCAATGACTACTGGGGCCAGGGAACGCTGGTCACCGTCTCCTCAGGTAAATCCATGCACAGTAATATGTGGCTGTGTCCACAGGGTCCATATTGGTCATGGTAAGGACCACCTGGCTTTTGGAGGTGTCCTTGGAGA
 
 #1339 vh3
@@ -164,15 +164,21 @@ TCAGAGACCTCACGCTGACCTGCACCGTCTCTGGGTTCTCACTCAGCAATGCTAGAATGGGTGTGAGCTGGATCCGTCAG
 GAACGGATAACTTCGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATCGAAGTGATAGCAGTGGCTGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGTAAA
 
 #1339 dh2
->IGHD2-2*01 10/3/1 IGHJ6*02  [IGH+] BUG
+>(IGHD2-2*01, IGHD2-2*02) 10/3/1 IGHJ6*02  [IGH+]
 ATTAGACAAAAACCCCCTGGAATCATAGTATCAGCAGGAGAACTAGCCAGAGACAGCAAGAGGGGACTCAGTGACTCCCGCGGGGACAGGAGGATTTTGTGGGGGCTCGTGTCACTGTGAGGATATTGTAGTAGTACCAGACCTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGT
 
 #1334 vh3
 >IGHV3-13*01 5/6/0 IGHD7-27*01 1/16/11 IGHJ4*02  [IGH] BUG
 GGAATGATCCTTCGTAGCTACGACATGCACTGGGTCCGCCAAGCTACAGGAAAAGGTCTGGAGTGGGTCTCAGCTATTGGTACTGCTGGTGACCCATACTATCCAGGCTCCGTGAAGGGCCGATTCACCATCTCCAGAGAAAATGCCAAGAACTCCTTGTATCTTCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCAGACACCCTAACTGGGGGGGGTTCCCTTGGGGGTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGTAA
 
+# IGHD2-2*01  GCGGGGACAGGAGGATTTTGTGGGGGCTCGTGTCACTGTGAGGATATTGTAGTAGTACCAGCTGCTATGCC
+#                                                |||||||||||||||||||||||||||||||||
+# read                                           CTGTGAGGATATTGTAGTAGTACCAGCTGTCATATTCGGGGATATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTCAAACC
+#                                                ||||||||||||||||||||||||||||||||||        ||||||||||||||||||||||||||||||||||||||||| 
+# IGHD2-2*02  GCGGGGACAGGAGGATTTTGTGGGGGCTCGTGTCACTGTGAGGATATTGTAGTAGTACCAGCTGCTATACC      |||||||||||||||||||||||||||||||||||||||||
+# IGHJ6*02                                                              ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCT
 #1334 dh2
->IGHD2-2*01 7/13/19 IGHJ6*02  [IGH+] BUG
+>IGHD2-2*02 2/TTCGGGGA/19 IGHJ6*02  [IGH+]
 ATTAGACAAACCCCCTGGAATCATAGTATCAGCAGGAGAACTAGCCAGAGACAGCAAGAGGGGACTCAGTGACTCCCGCGGGGACAGGAGGATTTTGTGGGGGCTCGTGTCACTGTGAGGATATTGTAGTAGTACCAGCTGTCATATTCGGGGATATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTCAAACC
 
 #1334 dh3
@@ -208,7 +214,7 @@ GCCAGGGATACTTCGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATAT
 GGCAATTCATCCTTCGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAAGAGGGGATGACTACAGTAACTACCAATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTA
 
 #gos268 dh2
->IGHD2-2*01 5/11/11 IGHJ6*02  [IGH+] BUG
+>(IGHD2-2*01, IGHD2-2*02) 5/11/11 IGHJ6*02  [IGH+]
 GGGTTTCGGACAAAAACCCCCTGGAAATCATAGTATCAGCAGGAGAACTAGCCAGAGACAGCAAGAGGGGACTCAGTGACTCCCGCGGGGACAGGAGGATTTTGTGGGGGCTCGTGTCACTGTGAGGATATTGTAGTAGTACCAGCTGCTCGGGGGCCAGTTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGT
 
 #gos268 dh4
@@ -260,7 +266,7 @@ GCTTGGAATCCTTCGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTA
 TTCCACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGAATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACTCCTTTGAAGCAGCTCGTCCGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCGTCAGGTAAAA
 
 #kw222 vh3
->IGHV3-13*01 6/9/12 IGHD2-2*01 3/4/0 IGHJ6*02  [IGH] BUG
+>IGHV3-13*01 6/9/12 (IGHD2-2*01, IGHD2-2*02) 3/4/0 IGHJ6*02  [IGH] BUG
 CGCATCCTTCGTAGCTACGACATGCACTGGGTCCGCCAAGCTACAGGAAAAGGTCTGGAGTGGGTCTCAGCTATTGGTACTGCTGGTGACACATACTATCCAGGCTCCGTGAAGGGCCGATTCACCATCTCCAGAGAAAATGCCAAGAACTCCTTGTATCTTCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCCCTCCGACCTAGTACCAGCTGCTATCCCTATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGT
 
 #kw221 vh3

algo/tests/unit-tests/testTools.cpp

@@ -50,10 +50,10 @@ void testOnlineBioReaderMaxNth() {
 
 
 void testFastaNbSequences() {
-  TAP_TEST_EQUAL(nb_sequences_in_file("../../germline/homo-sapiens/IGHV.fa"), 349, TEST_FASTA_NB_SEQUENCES, "ccc");
+  TAP_TEST_EQUAL(nb_sequences_in_file("../../germline/homo-sapiens/IGHV.fa"), 357, TEST_FASTA_NB_SEQUENCES, "ccc");
 
   int a1 = approx_nb_sequences_in_file("../../germline/homo-sapiens/IGHV.fa");
-  TAP_TEST(a1 >= 345 && a1 <= 355, TEST_FASTA_NB_SEQUENCES, "");
+  TAP_TEST(a1 >= 350 && a1 <= 370, TEST_FASTA_NB_SEQUENCES, "");
 
   int a2 = nb_sequences_in_file("data/Stanford_S22.fasta", true);
   TAP_TEST(a2 >= 13100 && a2 <= 13200, TEST_FASTA_NB_SEQUENCES, "");

demo/Demo-X5.fa

@@ -63,7 +63,7 @@ AACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAA
 
 
 # 0000-nck-TRB+
->TRBD2*02 8/10/2 TRBJ2-7*01  [TRB+]
+>TRBD2 8/10/2 TRBJ2-7*01  [TRB+]
 CTGCGCTTCCTGCCGCTGCCcaGTGGTTGGGGGAGGGGGACtaGCAGGGAGGAAACATTTTTGTATcaTGGTGTAACATTGTGGGGACTAGTGTCAGTCCCCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTTACAGGTAAGA
 
 

germline/germline_id

-52
+58

germline/homo-sapiens.g

 {
-    "ref": "http://www.vidjil.org/germlines/germline-52.tar.gz",
+    "ref": "http://www.vidjil.org/germlines/germline-58.tar.gz",
 
     "species": "Homo sapiens",
     "species_taxon_id": 9606,