Commit 2493de3d by Mathieu Giraud

### tests: .vdj.fa headers, 1-based positions

parent f38085e3
 ... @@ -7,4 +7,4 @@ \$ Find the good affects for the D segment, including a AMBIGUOUS k-mer, common w ... @@ -7,4 +7,4 @@ \$ Find the good affects for the D segment, including a AMBIGUOUS k-mer, common w 1:_ _ _ \\?.f.f.f.f.f.f _ _ _ _ 1:_ _ _ \\?.f.f.f.f.f.f _ _ _ _ \$ The windows found by the KmerSegmenter has a fairly good position \$ The windows found by the KmerSegmenter has a fairly good position 2: 0 162 179 219 2: 1 163 180 220
 ... @@ -13,7 +13,7 @@ \$ First sequence Stanford ... @@ -13,7 +13,7 @@ \$ First sequence Stanford # D: 0 del (left), 10 del (right) # D: 0 del (left), 10 del (right) # N2: CCCAAAC # N2: CCCAAAC # J: 8 del # J: 8 del 1:>lcl\\|FLN1FA002RWEZA.1\\|.*VDJ 0 164 175 195 203 242 IGHV3-48.0. 1/CGATCCCCCG/0 IGHD3-22.0. 10/CCCAAAC/8 IGHJ4.0. 1:>lcl\\|FLN1FA002RWEZA.1\\|.*VDJ 1 165 176 196 204 243 IGHV3-48.0. 1/CGATCCCCCG/0 IGHD3-22.0. 10/CCCAAAC/8 IGHJ4.0. \$ Second sequence Stanford \$ Second sequence Stanford # 165 169 180 # 165 169 180 ... @@ -28,7 +28,7 @@ \$ Second sequence Stanford ... @@ -28,7 +28,7 @@ \$ Second sequence Stanford # D: 7 del, 2 del # D: 7 del, 2 del # N2: C # N2: C # J: 0 del # J: 0 del 1:>lcl\\|FLN1FA001BLION.1\\|.*VDJ 0 165 169 180 182 232 IGHV1-3.01 1/TGG/7 IGHD6-13.0. 2/C/0 IGHJ3.0. 1:>lcl\\|FLN1FA001BLION.1\\|.*VDJ 1 166 170 181 183 233 IGHV1-3.01 1/TGG/7 IGHD6-13.0. 2/C/0 IGHJ3.0. \$ Third sequence Stanford \$ Third sequence Stanford # 169 177 208 214 # 169 177 208 214 ... @@ -44,4 +44,4 @@ \$ Third sequence Stanford ... @@ -44,4 +44,4 @@ \$ Third sequence Stanford # D : 0 del, 5 del # D : 0 del, 5 del # N2 : TGGGT # N2 : TGGGT # J : 10 del # J : 10 del 1:>lcl\\|FLN1FA002SGU3N.1\\|.*VDJ 0 169 177 208 214 251 IGHV3-9.0. 0/AAATTGG/0 IGHD3-16.0. 5/TGGGT/10 IGHJ4.0. 1:>lcl\\|FLN1FA002SGU3N.1\\|.*VDJ 1 170 178 209 215 252 IGHV3-9.0. 0/AAATTGG/0 IGHD3-16.0. 5/TGGGT/10 IGHJ4.0.
 ... @@ -12,10 +12,10 @@ \$ First sequence, easy segmentation (no error, few deletions at the windows, sma ... @@ -12,10 +12,10 @@ \$ First sequence, easy segmentation (no error, few deletions at the windows, sma # D3-16*01: gtattatgattacgtttgggggaGTTATGcttatacc # D3-16*01: gtattatgattacgtttgggggaGTTATGcttatacc # J5*01 : 1 acaactggttcgactcctggggccaaggaaccctggtcaccgtctcctcag # J5*01 : 1 acaactggttcgactcctggggccaaggaaccctggtcaccgtctcctcag # -2/CTTC/-3 -1/GTTA/5 # -2/CTTC/-3 -1/GTTA/5 1:^>seq1 \\+ VDJ 0 72 77 89 94 139 IGHV5-10-1.0[1-4] 2/CTTC/3 IGHD1-14.01 1/GTTA/5 IGHJ5.01 1:^>seq1 \\+ VDJ 1 73 78 90 95 140 IGHV5-10-1.0[1-4] 2/CTTC/3 IGHD1-14.01 1/GTTA/5 IGHJ5.01 # Note that a second D (D3-16*01) can be detected (6 common nucleotides, or even 7 with an overlap on the first D) # Note that a second D (D3-16*01) can be detected (6 common nucleotides, or even 7 with an overlap on the first D) # This is tested in segment_simul.should-vdj # This is tested in segment_simul.should-vdj \$ seq1_polyT is the same as seq1 but starts and ends with 10Ts, the recombination is in the middle. start position should not be 0 and end position should not be length-1 \$ seq1_polyT is the same as seq1 but starts and ends with 10Ts, the recombination is in the middle. start position should not be 0 and end position should not be length-1 f1:^>seq1_polyT \\+ VDJ 10 82 87 99 104 149 IGHV5-10-1.0[1-4] 2/CTTC/3 IGHD1-14.01 1/GTTA/5 IGHJ5.01 f1:^>seq1_polyT \\+ VDJ 11 83 88 100 105 150 IGHV5-10-1.0[1-4] 2/CTTC/3 IGHD1-14.01 1/GTTA/5 IGHJ5.01
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