hgvs/diff_test.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package hgvs
   6
   7 import (
   8         "strings"
   9         "testing"
  10
  11         "gopkg.in/check.v1"
  12 )
  13
  14 func Test(t *testing.T) { check.TestingT(t) }
  15
  16 type diffSuite struct{}
  17
  18 var _ = check.Suite(&diffSuite{})
  19
  20 func (s *diffSuite) TestDiff(c *check.C) {
  21         for _, trial := range []struct {
  22                 a      string
  23                 b      string
  24                 expect []string
  25         }{
  26                 {
  27                         a:      "aaaaaaaaaa",
  28                         b:      "aaaaCaaaaa",
  29                         expect: []string{"5A>C"},
  30                 },
  31                 {
  32                         a:      "aaaacGcaaa",
  33                         b:      "aaaaccaaa",
  34                         expect: []string{"6del"},
  35                 },
  36                 {
  37                         a:      "aaaacGGcaaa",
  38                         b:      "aaaaccaaa",
  39                         expect: []string{"6_7del"},
  40                 },
  41                 {
  42                         a:      "aaaac",
  43                         b:      "aaaa",
  44                         expect: []string{"5del"},
  45                 },
  46                 {
  47                         a:      "aaaa",
  48                         b:      "aaCaa",
  49                         expect: []string{"2_3insC"},
  50                 },
  51                 {
  52                         a:      "aaGGGtt",
  53                         b:      "aaCCCtt",
  54                         expect: []string{"3_5delinsCCC"},
  55                 },
  56                 {
  57                         a:      "aa",
  58                         b:      "aaCCC",
  59                         expect: []string{"2_3insCCC"},
  60                 },
  61                 {
  62                         a:      "aaGGttAAtttt",
  63                         b:      "aaCCttttttC",
  64                         expect: []string{"3G>C", "4G>C", "7_8del", "12_13insC"},
  65                 },
  66                 {
  67                         // without cleanup, diffmatchpatch solves this as {"3del", "=A", "4_5insA"}
  68                         a:      "aggaggggg",
  69                         b:      "agAaggggg",
  70                         expect: []string{"3G>A"},
  71                 },
  72                 {
  73                         // without cleanup, diffmatchpatch solves this as {"3_4del", "=A", "5_6insAA"}
  74                         a:      "agggaggggg",
  75                         b:      "agAAaggggg",
  76                         expect: []string{"3G>A", "4G>A"},
  77                 },
  78                 {
  79                         // without cleanup, diffmatchpatch solves this as {"3_4del", "=A", "5_6insCA"}
  80                         a:      "agggaggggg",
  81                         b:      "agACaggggg",
  82                         expect: []string{"3G>A", "4G>C"},
  83                 },
  84                 {
  85                         // without cleanup, diffmatchpatch solves this as {"3_7del", "=A", "8_9insAAACA"}
  86                         a:      "aggggggaggggg",
  87                         b:      "agAAAACaggggg",
  88                         expect: []string{"3_7delinsAAAAC"},
  89                 },
  90                 {
  91                         // without cleanup, diffmatchpatch solves this as {"3_7del", "=AAAA", "11_12insCAAAA"}
  92                         a:      "aggggggaaaaggggg",
  93                         b:      "agAAAACaaaaggggg",
  94                         expect: []string{"3_7delinsAAAAC"},
  95                 },
  96                 {
  97                         a:      "agggaggggg",
  98                         b:      "agCAaggggg",
  99                         expect: []string{"3G>C", "4G>A"},
 100                 },
 101                 {
 102                         a:      "agggg",
 103                         b:      "agAAg",
 104                         expect: []string{"3G>A", "4G>A"},
 105                 },
 106                 {
 107                         a:      "aggggg",
 108                         b:      "agAAAg",
 109                         expect: []string{"3_5delinsAAA"},
 110                 },
 111                 {
 112                         a:      "acgtgaa",
 113                         b:      "acTtgaa",
 114                         expect: []string{"3G>T"},
 115                 },
 116                 {
 117                         a:      "tcagaagac",
 118                         b:      "tcaAaagac",
 119                         expect: []string{"4G>A"},
 120                 },
 121                 {
 122                         a:      "tcagatggac",
 123                         b:      "tcaAaCggac",
 124                         expect: []string{"4G>A", "6T>C"},
 125                 },
 126                 {
 127                         a:      "tcagatggac",
 128                         b:      "tcaAaCggTc",
 129                         expect: []string{"4G>A", "6T>C", "9A>T"},
 130                 },
 131                 {
 132                         a:      "tcagatggac",
 133                         b:      "tcaAaCCggTc",
 134                         expect: []string{"4G>A", "6delinsCC", "9A>T"},
 135                 },
 136                 {
 137                         a:      "tcatagagac",
 138                         b:      "tcacaagac",
 139                         expect: []string{"4T>C", "6del"},
 140                 },
 141                 {
 142                         a:      "tcatcgagac",
 143                         b:      "tcGCcgagac",
 144                         expect: []string{"3A>G", "4T>C"},
 145                 },
 146                 {
 147                         a:      "tcatcgagac",
 148                         b:      "tcGCcggac",
 149                         expect: []string{"3A>G", "4T>C", "7del"},
 150                 },
 151                 {
 152                         // should delete leftmost
 153                         a:      "acgacaTTtttacac",
 154                         b:      "acgacatttacac",
 155                         expect: []string{"7_8del"},
 156                 },
 157                 {
 158                         // should delete leftmost
 159                         a:      "acgacATatatacac",
 160                         b:      "acgacatatacac",
 161                         expect: []string{"6_7del"},
 162                 },
 163                 {
 164                         // should insert leftmost
 165                         a:      "acgacatttacac",
 166                         b:      "acgacaTTtttacac",
 167                         expect: []string{"6_7insTT"},
 168                 },
 169                 {
 170                         // should insert leftmost
 171                         a:      "acgacatatacac",
 172                         b:      "acgacATatatacac",
 173                         expect: []string{"5_6insAT"},
 174                 },
 175                 {
 176                         a:      "cccacGATAtatcc",
 177                         b:      "cccactatcc",
 178                         expect: []string{"6_9del"},
 179                 },
 180                 {
 181                         a:      "acGATAtatcc",
 182                         b:      "actatcc",
 183                         expect: []string{"3_6del"},
 184                 },
 185                 {
 186                         a:      "acTTTTTatcc",
 187                         b:      "acGTTTatcc",
 188                         expect: []string{"3_4delinsG"},
 189                 },
 190                 {
 191                         a:      "acTTTTatcc",
 192                         b:      "acGTTTTTatcc",
 193                         expect: []string{"2_3insGT"},
 194                 },
 195                 {
 196                         a:      "aGACGGACAGGGCCCggatgcaa",
 197                         b:      "aggatgcaa",
 198                         expect: []string{"2_15del"},
 199                 },
 200                 {
 201                         a:      "aGACGGACAGGGCCCgt",
 202                         b:      "agt",
 203                         expect: []string{"2_15del"},
 204                 },
 205                 {
 206                         a:      "aGACGGACAGGGCCCgacggacagggccctag",
 207                         b:      "agacggacagggccctag",
 208                         expect: []string{"2_15del"},
 209                 },
 210                 {
 211                         a:      "cagacggacgtggggacccaGACGGACAGGGCCCggtaacc",
 212                         b:      "cagacggacgtggggacccaggtaacc",
 213                         expect: []string{"21_34del"},
 214                 },
 215                 {
 216                         a:      "cagacggacgtggggacccaggtaacc",
 217                         b:      "cagacggacgtggggacccaGACGGACAGGGCCCggtaacc",
 218                         expect: []string{"20_21insGACGGACAGGGCCC"},
 219                 },
 220                 {
 221                         a:      "aggGac",
 222                         b:      "aggAac",
 223                         expect: []string{"4G>A"},
 224                 },
 225                 {
 226                         a:      "atttTc",
 227                         b:      "atttCc",
 228                         expect: []string{"5T>C"},
 229                 },
 230                 {
 231                         a:      "atatataTAcgcgaa",
 232                         b:      "atatataCGcgcgaa",
 233                         expect: []string{"8T>C", "9A>G"},
 234                 },
 235                 {
 236                         a:      "gtaacccc",
 237                         b:      "gTAAtaacccc",
 238                         expect: []string{"1_2insTAA"},
 239                 },
 240                 {
 241                         a:      "cttaaa",
 242                         b:      "cTTCGttaaa",
 243                         expect: []string{"1_2insTTCG"},
 244                 },
 245                 {
 246                         a:      "tCAACAggg",
 247                         b:      "tCAggg",
 248                         expect: []string{"2_4del"},
 249                 },
 250                 {
 251                         a:      "caaAc",
 252                         b:      "caaCc",
 253                         expect: []string{"4A>C"},
 254                 },
 255                 {
 256                         a:      "aGGgaca",
 257                         b:      "agaca",
 258                         expect: []string{"2_3del"},
 259                 },
 260         } {
 261                 c.Log(trial)
 262                 var vars []string
 263                 diffs, _ := Diff(strings.ToUpper(trial.a), strings.ToUpper(trial.b), 0)
 264                 c.Logf("%v", diffs)
 265                 for _, v := range diffs {
 266                         vars = append(vars, v.String())
 267                 }
 268                 c.Check(vars, check.DeepEquals, trial.expect)
 269         }
 270 }