github.com/Schaudge/hts@v0.0.0-20240223063651-737b4d69d68c/sam/HG00096_1000_test.go (about) 1 package sam 2 3 import ( 4 "net/url" 5 "time" 6 ) 7 8 func init() { 9 for _, ref := range headerHG00096_1000.refs { 10 ref.owner = headerHG00096_1000 11 } 12 for _, rg := range headerHG00096_1000.rgs { 13 rg.owner = headerHG00096_1000 14 } 15 for _, prog := range headerHG00096_1000.progs { 16 prog.owner = headerHG00096_1000 17 } 18 } 19 20 var ( 21 // This is the header of the file 22 // ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/alignment/HG00096.unmapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam 23 // 24 // samtools view HG00096.unmapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam -H | sed -e 's/ \{7,8\}/\t/g'> HG00096_1000.sam # The sed sub is required due to broken format in original data. 25 // samtools view HG00096.unmapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam | head -n 1000 >> HG00096_1000.sam 26 // samtools view -Sb HG00096_1000.sam > HG00096_1000.bam 27 headerHG00096_1000 = &Header{ 28 Version: "1.0", 29 SortOrder: 3, 30 Comments: []string{ 31 "$known_indels_file(s) = ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.indels.sites.vcf.gz", 32 "$known_indels_file(s) .= ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.low_coverage_vqsr.20101123.indels.sites.vcf.gz", 33 "$known_sites_file(s) = ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.dbsnp.build135.snps.sites.vcf.gz", 34 }, 35 refs: []*Reference{ 36 { 37 id: 0, 38 name: "1", 39 lRef: 249250621, 40 md5: "\x1b\x22\xb9\x8c\xde\xb4\xa9\x30\x4c\xb5\xd4\x80\x26\xa8\x51\x28", 41 assemID: "NCBI37", 42 species: "Human", 43 uri: &url.URL{ 44 Scheme: "ftp", 45 Host: "ftp.1000genomes.ebi.ac.uk", 46 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 47 }, 48 }, 49 { 50 id: 1, 51 name: "2", 52 lRef: 243199373, 53 md5: "\xa0\xd9\x85\x1d\xa0\x04\x00\xde\xc1\x09\x8a\x92\x55\xac\x71\x2e", 54 assemID: "NCBI37", 55 species: "Human", 56 uri: &url.URL{ 57 Scheme: "ftp", 58 Host: "ftp.1000genomes.ebi.ac.uk", 59 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 60 }, 61 }, 62 { 63 id: 2, 64 name: "3", 65 lRef: 198022430, 66 md5: "\xfd\xfd\x81\x18\x49\xcc\x2f\xad\xeb\xc9\x29\xbb\x92\x59\x02\xe5", 67 assemID: "NCBI37", 68 species: "Human", 69 uri: &url.URL{ 70 Scheme: "ftp", 71 Host: "ftp.1000genomes.ebi.ac.uk", 72 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 73 }, 74 }, 75 { 76 id: 3, 77 name: "4", 78 lRef: 191154276, 79 md5: "\x23\xdc\xcd\x10\x68\x97\x54\x2a\xd8\x7d\x27\x65\xd2\x8a\x19\xa1", 80 assemID: "NCBI37", 81 species: "Human", 82 uri: &url.URL{ 83 Scheme: "ftp", 84 Host: "ftp.1000genomes.ebi.ac.uk", 85 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 86 }, 87 }, 88 { 89 id: 4, 90 name: "5", 91 lRef: 180915260, 92 md5: "\x07\x40\x17\x3d\xb9\xff\xd2\x64\xd7\x28\xf3\x27\x84\x84\x5c\xd7", 93 assemID: "NCBI37", 94 species: "Human", 95 uri: &url.URL{ 96 Scheme: "ftp", 97 Host: "ftp.1000genomes.ebi.ac.uk", 98 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 99 }, 100 }, 101 { 102 id: 5, 103 name: "6", 104 lRef: 171115067, 105 md5: "\x1d\x3a\x93\xa2\x48\xd9\x2a\x72\x9e\xe7\x64\x82\x3a\xcb\xbc\x6b", 106 assemID: "NCBI37", 107 species: "Human", 108 uri: &url.URL{ 109 Scheme: "ftp", 110 Host: "ftp.1000genomes.ebi.ac.uk", 111 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 112 }, 113 }, 114 { 115 id: 6, 116 name: "7", 117 lRef: 159138663, 118 md5: "\x61\x83\x66\xe9\x53\xd6\xaa\xad\x97\xdb\xe4\x77\x7c\x29\x37\x5e", 119 assemID: "NCBI37", 120 species: "Human", 121 uri: &url.URL{ 122 Scheme: "ftp", 123 Host: "ftp.1000genomes.ebi.ac.uk", 124 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 125 }, 126 }, 127 { 128 id: 7, 129 name: "8", 130 lRef: 146364022, 131 md5: "\x96\xf5\x14\xa9\x92\x9e\x41\x0c\x66\x51\x69\x7b\xde\xd5\x9a\xec", 132 assemID: "NCBI37", 133 species: "Human", 134 uri: &url.URL{ 135 Scheme: "ftp", 136 Host: "ftp.1000genomes.ebi.ac.uk", 137 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 138 }, 139 }, 140 { 141 id: 8, 142 name: "9", 143 lRef: 141213431, 144 md5: "\x3e\x27\x31\x17\xf1\x5e\x0a\x40\x0f\x01\x05\x5d\x9f\x39\x37\x68", 145 assemID: "NCBI37", 146 species: "Human", 147 uri: &url.URL{ 148 Scheme: "ftp", 149 Host: "ftp.1000genomes.ebi.ac.uk", 150 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 151 }, 152 }, 153 { 154 id: 9, 155 name: "10", 156 lRef: 135534747, 157 md5: "\x98\x8c\x28\xe0\x00\xe8\x4c\x26\xd5\x52\x35\x9a\xf1\xea\x2e\x1d", 158 assemID: "NCBI37", 159 species: "Human", 160 uri: &url.URL{ 161 Scheme: "ftp", 162 Host: "ftp.1000genomes.ebi.ac.uk", 163 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 164 }, 165 }, 166 { 167 id: 10, 168 name: "11", 169 lRef: 135006516, 170 md5: "\x98\xc5\x90\x49\xa2\xdf\x28\x5c\x76\xff\xb1\xc6\xdb\x8f\x8b\x96", 171 assemID: "NCBI37", 172 species: "Human", 173 uri: &url.URL{ 174 Scheme: "ftp", 175 Host: "ftp.1000genomes.ebi.ac.uk", 176 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 177 }, 178 }, 179 { 180 id: 11, 181 name: "12", 182 lRef: 133851895, 183 md5: "\x51\x85\x1a\xc0\xe1\xa1\x15\x84\x7a\xd3\x64\x49\xb0\x01\x58\x64", 184 assemID: "NCBI37", 185 species: "Human", 186 uri: &url.URL{ 187 Scheme: "ftp", 188 Host: "ftp.1000genomes.ebi.ac.uk", 189 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 190 }, 191 }, 192 { 193 id: 12, 194 name: "13", 195 lRef: 115169878, 196 md5: "\x28\x3f\x8d\x78\x92\xba\xa8\x1b\x51\x0a\x01\x57\x19\xca\x7b\x0b", 197 assemID: "NCBI37", 198 species: "Human", 199 uri: &url.URL{ 200 Scheme: "ftp", 201 Host: "ftp.1000genomes.ebi.ac.uk", 202 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 203 }, 204 }, 205 { 206 id: 13, 207 name: "14", 208 lRef: 107349540, 209 md5: "\x98\xf3\xca\xe3\x2b\x2a\x2e\x95\x24\xbc\x19\x81\x39\x27\x54\x2e", 210 assemID: "NCBI37", 211 species: "Human", 212 uri: &url.URL{ 213 Scheme: "ftp", 214 Host: "ftp.1000genomes.ebi.ac.uk", 215 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 216 }, 217 }, 218 { 219 id: 14, 220 name: "15", 221 lRef: 102531392, 222 md5: "\xe5\x64\x5a\x79\x4a\x82\x38\x21\x5b\x2c\xd7\x7a\xcb\x95\xa0\x78", 223 assemID: "NCBI37", 224 species: "Human", 225 uri: &url.URL{ 226 Scheme: "ftp", 227 Host: "ftp.1000genomes.ebi.ac.uk", 228 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 229 }, 230 }, 231 { 232 id: 15, 233 name: "16", 234 lRef: 90354753, 235 md5: "\xfc\x9b\x1a\x7b\x42\xb9\x7a\x86\x4f\x56\xb3\x48\xb0\x60\x95\xe6", 236 assemID: "NCBI37", 237 species: "Human", 238 uri: &url.URL{ 239 Scheme: "ftp", 240 Host: "ftp.1000genomes.ebi.ac.uk", 241 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 242 }, 243 }, 244 { 245 id: 16, 246 name: "17", 247 lRef: 81195210, 248 md5: "\x35\x1f\x64\xd4\xf4\xf9\xdd\xd4\x5b\x35\x33\x6a\xd9\x7a\xa6\xde", 249 assemID: "NCBI37", 250 species: "Human", 251 uri: &url.URL{ 252 Scheme: "ftp", 253 Host: "ftp.1000genomes.ebi.ac.uk", 254 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 255 }, 256 }, 257 { 258 id: 17, 259 name: "18", 260 lRef: 78077248, 261 md5: "\xb1\x5d\x4b\x2d\x29\xdd\xe9\xd3\xe4\xf9\x3d\x1d\x0f\x2c\xbc\x9c", 262 assemID: "NCBI37", 263 species: "Human", 264 uri: &url.URL{ 265 Scheme: "ftp", 266 Host: "ftp.1000genomes.ebi.ac.uk", 267 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 268 }, 269 }, 270 { 271 id: 18, 272 name: "19", 273 lRef: 59128983, 274 md5: "\x1a\xac\xd7\x1f\x30\xdb\x8e\x56\x18\x10\x91\x3e\x0b\x72\x63\x6d", 275 assemID: "NCBI37", 276 species: "Human", 277 uri: &url.URL{ 278 Scheme: "ftp", 279 Host: "ftp.1000genomes.ebi.ac.uk", 280 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 281 }, 282 }, 283 { 284 id: 19, 285 name: "20", 286 lRef: 63025520, 287 md5: "\x0d\xec\x96\x60\xec\x1e\xfa\xaf\x33\x28\x1c\x0d\x5e\xa2\x56\x0f", 288 assemID: "NCBI37", 289 species: "Human", 290 uri: &url.URL{ 291 Scheme: "ftp", 292 Host: "ftp.1000genomes.ebi.ac.uk", 293 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 294 }, 295 }, 296 { 297 id: 20, 298 name: "21", 299 lRef: 48129895, 300 md5: "\x29\x79\xa6\x08\x5b\xfe\x28\xe3\xad\x6f\x55\x2f\x36\x1e\xd7\x4d", 301 assemID: "NCBI37", 302 species: "Human", 303 uri: &url.URL{ 304 Scheme: "ftp", 305 Host: "ftp.1000genomes.ebi.ac.uk", 306 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 307 }, 308 }, 309 { 310 id: 21, 311 name: "22", 312 lRef: 51304566, 313 md5: "\xa7\x18\xac\xaa\x61\x35\xfd\xca\x83\x57\xd5\xbf\xe9\x42\x11\xdd", 314 assemID: "NCBI37", 315 species: "Human", 316 uri: &url.URL{ 317 Scheme: "ftp", 318 Host: "ftp.1000genomes.ebi.ac.uk", 319 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 320 }, 321 }, 322 { 323 id: 22, 324 name: "X", 325 lRef: 155270560, 326 md5: "\x7e\x0e\x2e\x58\x02\x97\xb7\x76\x4e\x31\xdb\xc8\x0c\x25\x40\xdd", 327 assemID: "NCBI37", 328 species: "Human", 329 uri: &url.URL{ 330 Scheme: "ftp", 331 Host: "ftp.1000genomes.ebi.ac.uk", 332 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 333 }, 334 }, 335 { 336 id: 23, 337 name: "Y", 338 lRef: 59373566, 339 md5: "\x1f\xa3\x47\x47\x50\xaf\x09\x48\xbd\xf9\x7d\x5a\x0e\xe5\x2e\x51", 340 assemID: "NCBI37", 341 species: "Human", 342 uri: &url.URL{ 343 Scheme: "ftp", 344 Host: "ftp.1000genomes.ebi.ac.uk", 345 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 346 }, 347 }, 348 { 349 id: 24, 350 name: "MT", 351 lRef: 16569, 352 md5: "\xc6\x8f\x52\x67\x4c\x9f\xb3\x3a\xef\x52\xdc\xf3\x99\x75\x55\x19", 353 assemID: "NCBI37", 354 species: "Human", 355 uri: &url.URL{ 356 Scheme: "ftp", 357 Host: "ftp.1000genomes.ebi.ac.uk", 358 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 359 }, 360 }, 361 { 362 id: 25, 363 name: "GL000207.1", 364 lRef: 4262, 365 md5: "\xf3\x81\x48\x41\xf1\x93\x9d\x3c\xa1\x90\x72\xd9\xe8\x9f\x3f\xd7", 366 assemID: "NCBI37", 367 species: "Human", 368 uri: &url.URL{ 369 Scheme: "ftp", 370 Host: "ftp.1000genomes.ebi.ac.uk", 371 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 372 }, 373 }, 374 { 375 id: 26, 376 name: "GL000226.1", 377 lRef: 15008, 378 md5: "\x1c\x1b\x2c\xd1\xfc\xcb\xc0\xa9\x9b\x6a\x44\x7f\xa2\x4d\x15\x04", 379 assemID: "NCBI37", 380 species: "Human", 381 uri: &url.URL{ 382 Scheme: "ftp", 383 Host: "ftp.1000genomes.ebi.ac.uk", 384 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 385 }, 386 }, 387 { 388 id: 27, 389 name: "GL000229.1", 390 lRef: 19913, 391 md5: "\xd0\xf4\x0e\xc8\x7d\xe3\x11\xd8\xe7\x15\xb5\x2e\x4c\x70\x62\xe1", 392 assemID: "NCBI37", 393 species: "Human", 394 uri: &url.URL{ 395 Scheme: "ftp", 396 Host: "ftp.1000genomes.ebi.ac.uk", 397 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 398 }, 399 }, 400 { 401 id: 28, 402 name: "GL000231.1", 403 lRef: 27386, 404 md5: "\xba\x88\x82\xce\x3a\x1e\xfa\x20\x80\xe5\xd2\x9b\x95\x65\x68\xa4", 405 assemID: "NCBI37", 406 species: "Human", 407 uri: &url.URL{ 408 Scheme: "ftp", 409 Host: "ftp.1000genomes.ebi.ac.uk", 410 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 411 }, 412 }, 413 { 414 id: 29, 415 name: "GL000210.1", 416 lRef: 27682, 417 md5: "\x85\x11\x06\xa7\x42\x38\x04\x41\x26\x13\x1c\xe2\xa8\xe5\x84\x7c", 418 assemID: "NCBI37", 419 species: "Human", 420 uri: &url.URL{ 421 Scheme: "ftp", 422 Host: "ftp.1000genomes.ebi.ac.uk", 423 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 424 }, 425 }, 426 { 427 id: 30, 428 name: "GL000239.1", 429 lRef: 33824, 430 md5: "\x99\x79\x5f\x15\x70\x2c\xae\xc4\xfa\x1c\x4e\x15\xf8\xa2\x9c\x07", 431 assemID: "NCBI37", 432 species: "Human", 433 uri: &url.URL{ 434 Scheme: "ftp", 435 Host: "ftp.1000genomes.ebi.ac.uk", 436 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 437 }, 438 }, 439 { 440 id: 31, 441 name: "GL000235.1", 442 lRef: 34474, 443 md5: "\x11\x8a\x25\xca\x21\x0c\xfb\xcd\xfb\x6c\x2e\xbb\x24\x9f\x96\x80", 444 assemID: "NCBI37", 445 species: "Human", 446 uri: &url.URL{ 447 Scheme: "ftp", 448 Host: "ftp.1000genomes.ebi.ac.uk", 449 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 450 }, 451 }, 452 { 453 id: 32, 454 name: "GL000201.1", 455 lRef: 36148, 456 md5: "\xdf\xb7\xe7\xec\x60\xff\xdc\xb8\x5c\xb3\x59\xea\x28\x45\x4e\xe9", 457 assemID: "NCBI37", 458 species: "Human", 459 uri: &url.URL{ 460 Scheme: "ftp", 461 Host: "ftp.1000genomes.ebi.ac.uk", 462 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 463 }, 464 }, 465 { 466 id: 33, 467 name: "GL000247.1", 468 lRef: 36422, 469 md5: "\x7d\xe0\x02\x26\xbb\x7d\xf1\xc5\x72\x76\xca\x6b\xaa\xba\xfd\x15", 470 assemID: "NCBI37", 471 species: "Human", 472 uri: &url.URL{ 473 Scheme: "ftp", 474 Host: "ftp.1000genomes.ebi.ac.uk", 475 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 476 }, 477 }, 478 { 479 id: 34, 480 name: "GL000245.1", 481 lRef: 36651, 482 md5: "\x89\xbc\x61\x96\x0f\x37\xd9\x4a\xbf\x0d\xf2\xd4\x81\xad\xa0\xec", 483 assemID: "NCBI37", 484 species: "Human", 485 uri: &url.URL{ 486 Scheme: "ftp", 487 Host: "ftp.1000genomes.ebi.ac.uk", 488 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 489 }, 490 }, 491 { 492 id: 35, 493 name: "GL000197.1", 494 lRef: 37175, 495 md5: "\x6f\x5e\xfd\xd3\x66\x43\xa9\xb8\xc8\xcc\xad\x6f\x2f\x1e\xdc\x7b", 496 assemID: "NCBI37", 497 species: "Human", 498 uri: &url.URL{ 499 Scheme: "ftp", 500 Host: "ftp.1000genomes.ebi.ac.uk", 501 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 502 }, 503 }, 504 { 505 id: 36, 506 name: "GL000203.1", 507 lRef: 37498, 508 md5: "\x96\x35\x8c\x32\x5f\xe0\xe7\x0b\xee\x73\x43\x6e\x8b\xb1\x4d\xbd", 509 assemID: "NCBI37", 510 species: "Human", 511 uri: &url.URL{ 512 Scheme: "ftp", 513 Host: "ftp.1000genomes.ebi.ac.uk", 514 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 515 }, 516 }, 517 { 518 id: 37, 519 name: "GL000246.1", 520 lRef: 38154, 521 md5: "\xe4\xaf\xcd\x31\x91\x2a\xf9\xd9\xc2\x54\x6a\xcf\x1c\xb2\x3a\xf2", 522 assemID: "NCBI37", 523 species: "Human", 524 uri: &url.URL{ 525 Scheme: "ftp", 526 Host: "ftp.1000genomes.ebi.ac.uk", 527 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 528 }, 529 }, 530 { 531 id: 38, 532 name: "GL000249.1", 533 lRef: 38502, 534 md5: "\x1d\x78\xab\xec\x37\xc1\x5f\xe2\x9a\x27\x5e\xb0\x8d\x5a\xf2\x36", 535 assemID: "NCBI37", 536 species: "Human", 537 uri: &url.URL{ 538 Scheme: "ftp", 539 Host: "ftp.1000genomes.ebi.ac.uk", 540 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 541 }, 542 }, 543 { 544 id: 39, 545 name: "GL000196.1", 546 lRef: 38914, 547 md5: 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"\x67\x43\xbd\x63\xb3\xff\x2b\x5b\x89\x85\xd8\x93\x3c\x53\x29\x0a", 1132 assemID: "NCBI37", 1133 species: "Human", 1134 uri: &url.URL{ 1135 Scheme: "ftp", 1136 Host: "ftp.1000genomes.ebi.ac.uk", 1137 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 1138 }, 1139 }, 1140 { 1141 id: 85, 1142 name: "hs37d5", 1143 lRef: 35477943, 1144 md5: "\x5b\x6a\x4b\x3a\x81\xa2\xd3\xc1\x34\xb7\xd1\x4b\xf6\xad\x39\xf1", 1145 assemID: "NCBI37", 1146 species: "Human", 1147 uri: &url.URL{ 1148 Scheme: "ftp", 1149 Host: "ftp.1000genomes.ebi.ac.uk", 1150 Path: "/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", 1151 }, 1152 }, 1153 }, 1154 rgs: []*ReadGroup{ 1155 { 1156 id: 0, 1157 name: "SRR062634", 1158 center: "WUGSC", 1159 description: "SRP001294", 1160 date: time.Time{}, 1161 flowOrder: "", 1162 keySeq: "", 1163 library: "2845856850", 1164 program: "", 1165 insertSize: 206, 1166 platform: "ILLUMINA", 1167 platformUnit: "", 1168 sample: "HG00096", 1169 }, 1170 { 1171 id: 1, 1172 name: "SRR062635", 1173 center: "WUGSC", 1174 description: "SRP001294", 1175 date: time.Time{}, 1176 flowOrder: "", 1177 keySeq: "", 1178 library: "2845856850", 1179 program: "", 1180 insertSize: 206, 1181 platform: "ILLUMINA", 1182 platformUnit: "", 1183 sample: "HG00096", 1184 }, 1185 { 1186 id: 2, 1187 name: "SRR062641", 1188 center: "WUGSC", 1189 description: "SRP001294", 1190 date: time.Time{}, 1191 flowOrder: "", 1192 keySeq: "", 1193 library: "2845856850", 1194 program: "", 1195 insertSize: 206, 1196 platform: "ILLUMINA", 1197 platformUnit: "", 1198 sample: "HG00096", 1199 }, 1200 }, 1201 progs: []*Program{ 1202 { 1203 id: 0, 1204 uid: "bwa_index", 1205 previous: "", 1206 name: "bwa", 1207 command: "bwa index -a bwtsw $reference_fasta", 1208 version: "0.5.9-r16", 1209 }, 1210 { 1211 id: 1, 1212 uid: "bwa_aln_fastq", 1213 previous: "bwa_index", 1214 name: "bwa", 1215 command: "bwa aln -q 15 -f $sai_file $reference_fasta $fastq_file", 1216 version: "0.5.9-r16", 1217 }, 1218 { 1219 id: 2, 1220 uid: "bwa_sam", 1221 previous: "bwa_aln_fastq", 1222 name: "bwa", 1223 command: "bwa sampe -a 618 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)", 1224 version: "0.5.9-r16", 1225 }, 1226 { 1227 id: 3, 1228 uid: "sam_to_fixed_bam", 1229 previous: "bwa_sam", 1230 name: "samtools", 1231 command: "samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file", 1232 version: "0.1.17 (r973:277)", 1233 }, 1234 { 1235 id: 4, 1236 uid: "gatk_target_interval_creator", 1237 previous: "sam_to_fixed_bam", 1238 name: "GenomeAnalysisTK", 1239 command: "java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s)", 1240 version: "1.2-29-g0acaf2d", 1241 }, 1242 { 1243 id: 5, 1244 uid: "bam_realignment_around_known_indels", 1245 previous: "gatk_target_interval_creator", 1246 name: "GenomeAnalysisTK", 1247 command: "java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing", 1248 version: "1.2-29-g0acaf2d", 1249 }, 1250 { 1251 id: 6, 1252 uid: "bam_count_covariates", 1253 previous: "bam_realignment_around_known_indels", 1254 name: "GenomeAnalysisTK", 1255 command: "java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate", 1256 version: "1.2-29-g0acaf2d", 1257 }, 1258 { 1259 id: 7, 1260 uid: "bam_recalibrate_quality_scores", 1261 previous: "bam_count_covariates", 1262 name: "GenomeAnalysisTK", 1263 command: "java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing", 1264 version: "1.2-29-g0acaf2d", 1265 }, 1266 { 1267 id: 8, 1268 uid: "bam_calculate_bq", 1269 previous: "bam_recalibrate_quality_scores", 1270 name: "samtools", 1271 command: "samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file", 1272 version: "0.1.17 (r973:277)", 1273 }, 1274 { 1275 id: 9, 1276 uid: "bam_merge", 1277 previous: "bam_calculate_bq", 1278 name: "picard", 1279 command: "java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT", 1280 version: "1.53", 1281 }, 1282 { 1283 id: 10, 1284 uid: "bam_mark_duplicates", 1285 previous: "bam_merge", 1286 name: "picard", 1287 command: "java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT", 1288 version: "1.53", 1289 }, 1290 { 1291 id: 11, 1292 uid: "bam_merge.1", 1293 previous: "bam_mark_duplicates", 1294 name: "picard", 1295 command: "java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT", 1296 version: "1.53", 1297 }, 1298 }, 1299 seenRefs: set{ 1300 "12": 11, 1301 "GL000238.1": 42, 1302 "GL000191.1": 58, 1303 "GL000227.1": 59, 1304 "GL000209.1": 63, 1305 "GL000246.1": 37, 1306 "GL000202.1": 43, 1307 "GL000233.1": 54, 1308 "GL000211.1": 67, 1309 "1": 0, 1310 "GL000207.1": 25, 1311 "GL000229.1": 27, 1312 "GL000236.1": 48, 1313 "GL000243.1": 50, 1314 "GL000214.1": 61, 1315 "2": 1, 1316 "GL000231.1": 28, 1317 "GL000244.1": 41, 1318 "GL000198.1": 56, 1319 "GL000213.1": 66, 1320 "GL000200.1": 79, 1321 "NC_007605": 84, 1322 "3": 2, 1323 "GL000234.1": 44, 1324 "GL000241.1": 49, 1325 "GL000216.1": 70, 1326 "GL000205.1": 72, 1327 "4": 3, 1328 "19": 18, 1329 "GL000196.1": 39, 1330 "GL000220.1": 65, 1331 "5": 4, 1332 "18": 17, 1333 "MT": 24, 1334 "GL000210.1": 29, 1335 "GL000247.1": 33, 1336 "GL000203.1": 36, 1337 "GL000232.1": 45, 1338 "6": 5, 1339 "GL000248.1": 40, 1340 "GL000222.1": 78, 1341 "GL000194.1": 81, 1342 "7": 6, 1343 "GL000201.1": 32, 1344 "GL000245.1": 34, 1345 "GL000230.1": 52, 1346 "GL000199.1": 68, 1347 "GL000212.1": 77, 1348 "8": 7, 1349 "15": 14, 1350 "X": 22, 1351 "GL000219.1": 73, 1352 "GL000224.1": 74, 1353 "GL000192.1": 83, 1354 "9": 8, 1355 "14": 13, 1356 "Y": 23, 1357 "GL000197.1": 35, 1358 "GL000221.1": 62, 1359 "17": 16, 1360 "GL000226.1": 26, 1361 "GL000239.1": 30, 1362 "GL000208.1": 57, 1363 "hs37d5": 85, 1364 "16": 15, 1365 "GL000249.1": 38, 1366 "GL000223.1": 75, 1367 "GL000195.1": 76, 1368 "11": 10, 1369 "20": 19, 1370 "GL000206.1": 46, 1371 "GL000242.1": 51, 1372 "GL000237.1": 53, 1373 "GL000228.1": 60, 1374 "GL000215.1": 71, 1375 "10": 9, 1376 "21": 20, 1377 "GL000218.1": 64, 1378 "GL000193.1": 80, 1379 "GL000225.1": 82, 1380 "13": 12, 1381 "22": 21, 1382 "GL000235.1": 31, 1383 "GL000240.1": 47, 1384 "GL000204.1": 55, 1385 "GL000217.1": 69, 1386 }, 1387 seenGroups: set{ 1388 "SRR062634": 0, 1389 "SRR062635": 1, 1390 "SRR062641": 2, 1391 }, 1392 seenProgs: set{ 1393 "bwa_index": 0, 1394 "sam_to_fixed_bam": 3, 1395 "bam_realignment_around_known_indels": 5, 1396 "bam_recalibrate_quality_scores": 7, 1397 "bam_calculate_bq": 8, 1398 "bam_merge": 9, 1399 "bam_mark_duplicates": 10, 1400 "bwa_aln_fastq": 1, 1401 "bwa_sam": 2, 1402 "gatk_target_interval_creator": 4, 1403 "bam_count_covariates": 6, 1404 "bam_merge.1": 11, 1405 }, 1406 } 1407 )