Mercurial > repos > iuc > biscot

comparison test-data/reference_cmap_file.cmap @ 0:ef4b5ce71745 draft default tip

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planemo upload for repository https://github.com/bgruening/iuc/tree/master/tools/biscot commit cce7b9b092030d3bb23a706ca3bf2dece9c20b5f
author iuc
date Fri, 06 Jan 2023 22:10:44 +0000
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-1:000000000000 0:ef4b5ce71745
1 # hostname=6d61d934e61b
2 # $ cd /HybridScaffold; /RefAligner/amd2/RefAligner -o /data/jwd03f/main/053/913/53913897/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD -stdout -stderr -i /data/jwd03f/main/053/913/53913897/working/assignAlignType/assignAlignType_q.cmap -ref /data/jwd03f/main/053/913/53913897/working/align_final/step2.hybrid.cmap -maxmem 250 -maxthreads 24 -maxvirtmem 250 -RAmem 3 1 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 6 -deltaY 6 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 24 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 14 -AlignRes 2. -outlierExtend 6 24 -Kmax 6 -resEstimate -BestRef 1 -f -mres 0.9
3 # CompileDir= /home/users/sqa01/RefAlignerBuild/branches/12432.12463rel/12432.12463rel CompileCmd=/opt/gcc-9.3.0/bin/g++ -B/opt/binutils-2.34 -fopenmp -Ofast -march=znver2 -mavx2 -mfpmath=sse -DUSE_PFLOAT=1 -DUSE_RFLOAT=1 -DUSE_SSE=1 -DUSE_MFLOAT=1 -DUSE_EPOW=2 -I/home/users8/tanantharaman/sleef-081120/build/include -I/opt/glibc-2.31/include -DUSE_STATIC -freciprocal-math -fno-signed-zeros -fno-trapping-math -fno-tree-vectorize -mtune=znver2 -fno-lto-odr-type-merging -DRELEASE=1 -std=gnu++98 -Wl,--dynamic-linker=/opt/glibc-2.31/lib/ld-linux-x86-64.so.2 -Wl,--rpath=/opt/glibc-2.31/lib -Wl,--rpath=/opt/gcc-9.3.0/lib64 -lsleefinline -lrt -lmvec -L/home/users8/tanantharaman/sleef-081120/build/lib -L/opt/glibc-2.31/lib -L/opt/gcc-9.3.0/lib64 -static -static-libstdc++ -static-libgcc -s SVNversion=12463 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/12432/RefAligner.cpp 12458 2021-10-24 00:56:45Z tanantharaman $
4 # FLAGS: USE_SSE=1 USE_AVX=1 USE_MIC=0 USE_PFLOAT=1 USE_RFLOAT=1 USE_MFLOAT=1 USE_EPOW=2 DEBUG=1 VERB=1
5 # CMAP File Version: 0.1
6 # Label Channels: 1
7 # Nickase Recognition Site 1: gctcttc
8 # Number of Consensus Maps: 1
9 # StdDev refers to the interval between the current site and the next site
10 #h CMapId ContigLength NumSites SiteID LabelChannel Position StdDev Coverage Occurrence Mask
11 #f int float int int int float float float float Hex
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575 1 4753350.0 624 564 1 4244962.0 0.0 1.0 1.0 0
576 1 4753350.0 624 565 1 4253166.0 0.0 1.0 1.0 0
577 1 4753350.0 624 566 1 4254649.0 0.0 1.0 1.0 0
578 1 4753350.0 624 567 1 4255627.0 0.0 1.0 1.0 0
579 1 4753350.0 624 568 1 4256548.0 0.0 1.0 1.0 0
580 1 4753350.0 624 569 1 4282081.0 0.0 1.0 1.0 0
581 1 4753350.0 624 570 1 4307180.0 0.0 1.0 1.0 0
582 1 4753350.0 624 571 1 4307943.0 0.0 1.0 1.0 0
583 1 4753350.0 624 572 1 4344738.0 0.0 1.0 1.0 0
584 1 4753350.0 624 573 1 4348150.0 0.0 1.0 1.0 0
585 1 4753350.0 624 574 1 4378210.0 0.0 1.0 1.0 0
586 1 4753350.0 624 575 1 4388767.0 0.0 1.0 1.0 0
587 1 4753350.0 624 576 1 4393246.5 0.0 1.0 1.0 0
588 1 4753350.0 624 577 1 4396436.0 0.0 1.0 1.0 0
589 1 4753350.0 624 578 1 4425979.0 0.0 1.0 1.0 0
590 1 4753350.0 624 579 1 4430102.0 0.0 1.0 1.0 0
591 1 4753350.0 624 580 1 4434980.0 0.0 1.0 1.0 0
592 1 4753350.0 624 581 1 4441066.0 0.0 1.0 1.0 0
593 1 4753350.0 624 582 1 4447044.0 0.0 1.0 1.0 0
594 1 4753350.0 624 583 1 4455184.0 0.0 1.0 1.0 0
595 1 4753350.0 624 584 1 4458855.0 0.0 1.0 1.0 0
596 1 4753350.0 624 585 1 4465699.0 0.0 1.0 1.0 0
597 1 4753350.0 624 586 1 4470564.0 0.0 1.0 1.0 0
598 1 4753350.0 624 587 1 4477348.0 0.0 1.0 1.0 0
599 1 4753350.0 624 588 1 4496647.0 0.0 1.0 1.0 0
600 1 4753350.0 624 589 1 4500425.0 0.0 1.0 1.0 0
601 1 4753350.0 624 590 1 4503201.5 0.0 1.0 1.0 0
602 1 4753350.0 624 591 1 4504903.0 0.0 1.0 0.0 0
603 1 4753350.0 624 592 1 4517141.0 0.0 1.0 1.0 0
604 1 4753350.0 624 593 1 4531397.0 0.0 1.0 1.0 0
605 1 4753350.0 624 594 1 4541380.0 0.0 1.0 1.0 0
606 1 4753350.0 624 595 1 4567270.0 0.0 1.0 1.0 0
607 1 4753350.0 624 596 1 4569921.0 0.0 1.0 1.0 0
608 1 4753350.0 624 597 1 4577868.0 0.0 1.0 1.0 0
609 1 4753350.0 624 598 1 4590892.0 0.0 1.0 0.0 0
610 1 4753350.0 624 599 1 4592022.0 0.0 1.0 1.0 0
611 1 4753350.0 624 600 1 4604106.0 0.0 1.0 1.0 0
612 1 4753350.0 624 601 1 4632897.0 0.0 1.0 1.0 0
613 1 4753350.0 624 602 1 4653877.0 0.0 1.0 1.0 0
614 1 4753350.0 624 603 1 4657868.0 0.0 1.0 1.0 0
615 1 4753350.0 624 604 1 4658400.0 0.0 1.0 1.0 0
616 1 4753350.0 624 605 1 4665746.0 0.0 1.0 1.0 0
617 1 4753350.0 624 606 1 4668337.0 0.0 1.0 1.0 0
618 1 4753350.0 624 607 1 4677111.0 0.0 1.0 1.0 0
619 1 4753350.0 624 608 1 4680578.5 0.0 1.0 1.0 0
620 1 4753350.0 624 609 1 4681147.0 0.0 1.0 1.0 0
621 1 4753350.0 624 610 1 4683691.0 0.0 1.0 1.0 0
622 1 4753350.0 624 611 1 4698978.0 0.0 1.0 1.0 0
623 1 4753350.0 624 612 1 4700428.0 0.0 1.0 1.0 0
624 1 4753350.0 624 613 1 4702436.5 0.0 1.0 1.0 0
625 1 4753350.0 624 614 1 4705006.0 0.0 1.0 1.0 0
626 1 4753350.0 624 615 1 4708196.0 0.0 1.0 1.0 0
627 1 4753350.0 624 616 1 4724778.0 0.0 1.0 1.0 0
628 1 4753350.0 624 617 1 4725417.0 0.0 1.0 1.0 0
629 1 4753350.0 624 618 1 4727183.0 0.0 1.0 1.0 0
630 1 4753350.0 624 619 1 4727700.0 0.0 1.0 1.0 0
631 1 4753350.0 624 620 1 4731209.0 0.0 1.0 1.0 0
632 1 4753350.0 624 621 1 4732628.0 0.0 1.0 0.0 0
633 1 4753350.0 624 622 1 4740112.0 0.0 1.0 1.0 0
634 1 4753350.0 624 623 1 4743710.0 0.0 1.0 1.0 0
635 1 4753350.0 624 624 1 4747257.5 0.0 1.0 1.0 0
636 1 4753350.0 624 625 0 4753350.0 0.0 1.0 1.0 10