Mercurial > repos > portiahollyoak > breakdancer_max
changeset 4:eb2770895305 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 6c005d5d29cd9684fee5474a7adac676fc27ecb3-dirty
| author | portiahollyoak |
|---|---|
| date | Mon, 23 May 2016 05:40:41 -0400 |
| parents | 8fee2dac93a4 |
| children | c2bb6aa52c74 |
| files | test-data/X_1000000_Hum1.tab test-data/breakdancer_config_X_100000 |
| diffstat | 2 files changed, 128 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/X_1000000_Hum1.tab Mon May 23 05:40:41 2016 -0400 @@ -0,0 +1,127 @@ +#Software: r2015.11-56-gbca69f3-unstable-dirty (commit r2015.11-56-gbca69f3-dirty) +#Command: breakdancer-max breakdancer_config_X_100000 -g X_10000000_Hum1.bed +#Library Statistics: +#X_10000000_Hum1.bam mean:227 std:98 uppercutoff:521 lowercutoff:0 readlen:125 library:X_10000000_Hum1 reflen:999972 seqcov:11.8552 phycov:10.7645 1:62 2:3551 4:2764 8:106 32:1416 +#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib X_10000000_Hum1.bam +X 131684 5+0- X 131981 1+7- DEL 340 65 5 X_10000000_Hum1.bam|5 2.98 +X 142444 7+4- X 142488 7+4- ITX -102 67 4 X_10000000_Hum1.bam|4 NA +X 142690 3+2- X 142709 3+2- ITX -104 46 2 X_10000000_Hum1.bam|2 NA +X 145921 3+0- X 146395 0+2- DEL 526 32 2 X_10000000_Hum1.bam|2 2.49 +X 151718 7+0- X 151998 0+4- DEL 331 41 4 X_10000000_Hum1.bam|4 3.95 +X 155647 5+3- X 155671 5+3- ITX -102 60 3 X_10000000_Hum1.bam|3 NA +X 157963 3+1- X 158377 0+3- DEL 432 35 3 X_10000000_Hum1.bam|3 4.62 +X 158261 4+4- X 158489 0+6- DEL 306 54 4 X_10000000_Hum1.bam|4 3.70 +X 159597 3+2- X 159984 0+3- DEL 437 35 3 X_10000000_Hum1.bam|3 2.29 +X 184550 2+4- X 184570 2+4- ITX -107 45 2 X_10000000_Hum1.bam|2 NA +X 185570 10+8- X 185591 10+8- ITX -103 99 8 X_10000000_Hum1.bam|8 NA +X 186648 9+18- X 186959 6+6- ITX -171 74 6 X_10000000_Hum1.bam|6 0.95 +X 186648 9+18- X 187326 18+8- ITX 178 99 12 X_10000000_Hum1.bam|12 4.88 +X 186821 6+6- X 187326 18+8- ITX 20 38 4 X_10000000_Hum1.bam|4 4.55 +X 188119 11+2- X 188178 11+2- ITX -104 32 2 X_10000000_Hum1.bam|2 NA +X 188298 11+2- X 188541 0+5- DEL 326 34 3 X_10000000_Hum1.bam|3 2.15 +X 254834 1+10- X 254884 1+10- INV -147 99 3 X_10000000_Hum1.bam|3 NA +X 268244 7+1- X 268508 7+7- DEL 324 71 7 X_10000000_Hum1.bam|7 2.58 +X 268716 7+7- X 269103 1+5- DEL 446 47 5 X_10000000_Hum1.bam|5 5.24 +X 269032 2+2- X 269471 0+2- DEL 376 34 2 X_10000000_Hum1.bam|2 2.98 +X 269503 8+0- X 269803 0+4- DEL 306 45 3 X_10000000_Hum1.bam|3 2.51 +X 274164 4+4- X 274175 4+4- ITX -105 95 4 X_10000000_Hum1.bam|4 NA +X 280215 3+0- X 280484 2+3- DEL 321 33 3 X_10000000_Hum1.bam|3 2.39 +X 282107 13+0- X 282350 0+13- DEL 304 99 13 X_10000000_Hum1.bam|13 4.82 +X 295796 5+0- X 303476 4+12- DEL 7676 72 5 X_10000000_Hum1.bam|5 0.09 +X 295964 9+0- X 303476 4+12- DEL 7538 91 7 X_10000000_Hum1.bam|7 0.06 +X 307512 6+0- X 307815 0+3- DEL 321 43 3 X_10000000_Hum1.bam|3 2.54 +X 307512 6+0- X 308007 0+10- DEL 512 35 3 X_10000000_Hum1.bam|3 2.06 +X 316962 11+4- X 317228 0+7- DEL 383 61 7 X_10000000_Hum1.bam|7 4.48 +X 329258 9+4- X 329314 9+4- ITX -102 61 4 X_10000000_Hum1.bam|4 NA +X 332888 2+3- X 332899 2+3- ITX -105 52 2 X_10000000_Hum1.bam|2 NA +X 339370 4+0- X 339690 0+4- DEL 384 47 4 X_10000000_Hum1.bam|4 2.59 +X 343414 8+4- X 343434 8+4- ITX -104 83 4 X_10000000_Hum1.bam|4 NA +X 353226 4+6- X 353254 4+6- ITX -102 76 4 X_10000000_Hum1.bam|4 NA +X 358309 11+5- X 358377 11+5- ITX -105 72 5 X_10000000_Hum1.bam|5 NA +X 363873 2+0- X 364155 0+2- DEL 320 33 2 X_10000000_Hum1.bam|2 3.15 +X 366958 5+0- X 367228 0+8- DEL 319 48 5 X_10000000_Hum1.bam|5 2.33 +X 368221 4+2- X 368271 4+2- ITX -102 34 2 X_10000000_Hum1.bam|2 NA +X 393353 3+0- X 393689 0+3- DEL 405 37 3 X_10000000_Hum1.bam|3 2.91 +X 394653 8+5- X 394702 8+5- ITX -104 81 5 X_10000000_Hum1.bam|5 NA +X 394822 8+5- X 395256 5+3- DEL 452 34 3 X_10000000_Hum1.bam|3 2.97 +X 398500 3+4- X 398517 3+4- ITX -104 66 3 X_10000000_Hum1.bam|3 NA +X 399821 4+0- X 400117 0+4- DEL 347 57 4 X_10000000_Hum1.bam|4 1.93 +X 414461 5+1- X 414833 3+2- DEL 390 32 2 X_10000000_Hum1.bam|2 2.74 +X 418595 8+3- X 418888 0+4- DEL 355 40 4 X_10000000_Hum1.bam|4 5.21 +X 419577 3+3- X 419588 3+3- ITX -105 52 2 X_10000000_Hum1.bam|2 NA +X 426627 9+5- X 426679 9+5- ITX -102 79 5 X_10000000_Hum1.bam|5 NA +X 428545 14+0- X 434702 0+8- DEL 6151 59 5 X_10000000_Hum1.bam|5 0.06 +X 441688 7+12- X 441764 7+12- ITX -105 85 6 X_10000000_Hum1.bam|6 NA +X 445015 7+0- X 445376 0+3- DEL 390 57 3 X_10000000_Hum1.bam|3 4.91 +X 449622 3+0- X 449909 0+3- DEL 332 36 3 X_10000000_Hum1.bam|3 1.61 +X 456767 2+1- X 457103 1+2- DEL 354 41 2 X_10000000_Hum1.bam|2 3.61 +X 458386 6+2- X 458412 6+2- ITX -103 42 2 X_10000000_Hum1.bam|2 NA +X 471097 5+0- X 471427 2+5- DEL 348 43 3 X_10000000_Hum1.bam|3 3.28 +X 486082 4+3- X 486116 4+3- ITX -103 55 3 X_10000000_Hum1.bam|3 NA +X 488923 4+0- X 489190 1+10- DEL 335 39 4 X_10000000_Hum1.bam|4 4.03 +X 495979 7+1- X 496291 0+3- DEL 389 36 3 X_10000000_Hum1.bam|3 6.98 +X 496048 7+0- X 496370 0+9- DEL 434 44 4 X_10000000_Hum1.bam|4 6.25 +X 497786 7+5- X 497877 7+5- ITX -103 51 4 X_10000000_Hum1.bam|4 NA +X 503489 2+1- X 503867 0+2- DEL 404 42 2 X_10000000_Hum1.bam|2 3.35 +X 508754 2+9- X 509277 8+0- ITX 46 99 8 X_10000000_Hum1.bam|8 4.52 +X 508871 4+5- X 508926 4+5- ITX -190 62 4 X_10000000_Hum1.bam|4 NA +X 511090 6+0- X 511323 9+5- DEL 298 52 5 X_10000000_Hum1.bam|5 1.55 +X 525277 5+6- X 525331 5+6- ITX -106 62 4 X_10000000_Hum1.bam|4 NA +X 544176 3+2- X 544203 3+2- ITX -103 41 2 X_10000000_Hum1.bam|2 NA +X 547108 0+4- X 547119 0+4- INV -172 99 2 X_10000000_Hum1.bam|2 NA +X 576352 6+3- X 576374 6+3- ITX -102 62 3 X_10000000_Hum1.bam|3 NA +X 583435 4+2- X 583796 0+4- DEL 379 52 4 X_10000000_Hum1.bam|4 2.81 +X 606834 7+5- X 606854 7+5- ITX -102 99 5 X_10000000_Hum1.bam|5 NA +X 608448 3+1- X 608799 2+3- DEL 397 36 3 X_10000000_Hum1.bam|3 2.15 +X 608626 8+2- X 608655 8+2- ITX -102 40 2 X_10000000_Hum1.bam|2 NA +X 608775 8+2- X 609044 5+3- DEL 322 37 3 X_10000000_Hum1.bam|3 2.28 +X 608775 8+2- X 609151 0+3- DEL 348 39 3 X_10000000_Hum1.bam|3 2.51 +X 611710 7+8- X 611742 7+8- ITX -103 99 6 X_10000000_Hum1.bam|6 NA +X 616393 7+8- X 616469 7+8- ITX -105 70 5 X_10000000_Hum1.bam|5 NA +X 618395 6+0- X 618664 0+4- DEL 298 59 4 X_10000000_Hum1.bam|4 2.71 +X 636124 3+0- X 636495 0+2- DEL 320 39 2 X_10000000_Hum1.bam|2 2.71 +X 646679 0+5- X 646771 0+5- INV -110 75 2 X_10000000_Hum1.bam|2 NA +X 655838 5+4- X 655862 5+4- ITX -105 79 4 X_10000000_Hum1.bam|4 NA +X 661291 13+6- X 661341 13+6- ITX -103 97 6 X_10000000_Hum1.bam|6 NA +X 669443 7+6- X 669472 7+6- ITX -105 99 6 X_10000000_Hum1.bam|6 NA +X 679247 2+0- X 679533 0+2- DEL 320 36 2 X_10000000_Hum1.bam|2 1.77 +X 681969 6+0- X 682249 0+6- DEL 306 79 6 X_10000000_Hum1.bam|6 1.16 +X 686028 3+2- X 686037 3+2- ITX -102 55 2 X_10000000_Hum1.bam|2 NA +X 687744 7+4- X 687842 7+4- ITX -105 37 3 X_10000000_Hum1.bam|3 NA +X 693329 10+4- X 693392 10+4- ITX -105 59 4 X_10000000_Hum1.bam|4 NA +X 701901 5+12- X 701966 5+12- ITX -103 74 5 X_10000000_Hum1.bam|5 NA +X 701901 5+12- X 703053 6+1- ITX 617 78 6 X_10000000_Hum1.bam|6 4.21 +X 712176 6+9- X 712264 6+9- ITX -102 66 5 X_10000000_Hum1.bam|5 NA +X 729606 6+0- X 729839 0+6- DEL 296 73 6 X_10000000_Hum1.bam|6 1.55 +X 739865 3+1- X 740260 0+2- DEL 368 32 2 X_10000000_Hum1.bam|2 2.17 +X 745932 4+0- X 746280 0+4- DEL 384 65 4 X_10000000_Hum1.bam|4 3.24 +X 750098 7+3- X 750122 7+3- ITX -102 60 3 X_10000000_Hum1.bam|3 NA +X 769626 3+4- X 769655 3+4- ITX -103 57 3 X_10000000_Hum1.bam|3 NA +X 783709 4+2- X 783748 4+2- ITX -103 37 2 X_10000000_Hum1.bam|2 NA +X 801585 4+3- X 801633 4+3- ITX -102 49 3 X_10000000_Hum1.bam|3 NA +X 811468 13+13- X 811480 13+13- ITX -105 99 13 X_10000000_Hum1.bam|13 NA +X 812253 8+2- X 817895 2+16- DEL 5758 70 7 X_10000000_Hum1.bam|7 0.11 +X 812378 8+0- X 817895 2+16- DEL 5555 95 8 X_10000000_Hum1.bam|8 0.10 +X 819693 3+0- X 820007 1+4- DEL 369 33 3 X_10000000_Hum1.bam|3 2.28 +X 820478 8+5- X 820521 8+5- ITX -105 84 5 X_10000000_Hum1.bam|5 NA +X 821851 6+3- X 821882 6+3- ITX -102 56 3 X_10000000_Hum1.bam|3 NA +X 826401 2+3- X 826801 1+2- DEL 418 33 2 X_10000000_Hum1.bam|2 2.35 +X 827663 15+0- X 835391 0+6- DEL 7844 58 6 X_10000000_Hum1.bam|6 0.14 +X 827663 15+0- X 835497 0+6- DEL 7910 53 6 X_10000000_Hum1.bam|6 0.20 +X 836831 3+0- X 837172 0+3- DEL 375 44 3 X_10000000_Hum1.bam|3 2.33 +X 838911 2+3- X 838923 2+3- ITX -104 51 2 X_10000000_Hum1.bam|2 NA +X 842752 5+7- X 842773 5+7- ITX -105 99 5 X_10000000_Hum1.bam|5 NA +X 867585 3+2- X 867902 0+3- DEL 348 43 3 X_10000000_Hum1.bam|3 1.45 +X 869931 9+9- X 869946 9+9- ITX -103 99 9 X_10000000_Hum1.bam|9 NA +X 808851 0+5- X 896693 0+5- INV 87616 99 5 X_10000000_Hum1.bam|5 2.04 +X 882462 5+0- X 882732 0+5- DEL 311 55 5 X_10000000_Hum1.bam|5 3.24 +X 886628 7+0- X 886945 2+7- DEL 360 92 7 X_10000000_Hum1.bam|7 2.41 +X 893058 4+7- X 893162 4+7- ITX -104 49 4 X_10000000_Hum1.bam|4 NA +X 904956 6+0- X 905302 0+5- DEL 368 74 5 X_10000000_Hum1.bam|5 1.40 +X 906794 7+0- X 908529 0+12- DEL 1714 94 7 X_10000000_Hum1.bam|7 1.35 +X 922108 4+3- X 922141 4+3- ITX -102 55 3 X_10000000_Hum1.bam|3 NA +X 949787 3+2- X 949812 3+2- ITX -103 42 2 X_10000000_Hum1.bam|2 NA +X 970591 7+0- X 970927 0+7- DEL 319 87 7 X_10000000_Hum1.bam|7 2.77 +X 971930 3+5- X 972019 3+5- ITX -102 39 3 X_10000000_Hum1.bam|3 NA +X 976376 7+0- X 976723 0+7- DEL 419 78 7 X_10000000_Hum1.bam|7 1.99 +X 999900 11+3- X 999950 11+3- ITX -104 48 3 X_10000000_Hum1.bam|3 NA
--- a/test-data/breakdancer_config_X_100000 Mon May 23 05:19:22 2016 -0400 +++ b/test-data/breakdancer_config_X_100000 Mon May 23 05:40:41 2016 -0400 @@ -1,1 +1,1 @@ -map:../HUM_BAM_dm6fasta/Hum1.bwa.bam mean:227 std:98 readlen:125 sample:HUM1 exe:samtools view +map:X_10000000_Hum1.bam mean:227 std:98 readlen:125 sample:X_10000000_Hum1 exe:samtools view