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Commit 1f431153 authored by Mikaël Salson's avatar Mikaël Salson
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should-get-tests: Alternative for identical sequences 

Sequences are identical (on the region where the read is). Therefore we have
to offer alternatives.

It is not clear why the bugs are new.
parent 064521ab
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Showing with 13 additions and 7 deletions
algo/tests/should-vdj-tests/0000-nck-TRB+.should-vdj.fa
View file @ 1f431153
>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/gosh-igh.should-vdj.fa
View file @ 1f431153
......@@ -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
......@@ -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
......@@ -164,7 +164,7 @@ 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
......@@ -208,7 +208,7 @@ 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 +260,7 @@ 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
......
demo/Demo-X5.fa
View file @ 1f431153
......@@ -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
......
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