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Add support for minimap as an overlapper option
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,128 @@ | ||
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| /****************************************************************************** | ||
| * | ||
| * This file is part of canu, a software program that assembles whole-genome | ||
| * sequencing reads into contigs. | ||
| * | ||
| * This software is based on: | ||
| * 'Celera Assembler' (http://wgs-assembler.sourceforge.net) | ||
| * the 'kmer package' (http://kmer.sourceforge.net) | ||
| * both originally distributed by Applera Corporation under the GNU General | ||
| * Public License, version 2. | ||
| * | ||
| * Canu branched from Celera Assembler at its revision 4587. | ||
| * Canu branched from the kmer project at its revision 1994. | ||
| * | ||
| * Modifications by: | ||
| * | ||
| * Brian P. Walenz from 2015-MAR-27 to 2015-JUN-25 | ||
| * are Copyright 2015 Battelle National Biodefense Institute, and | ||
| * are subject to the BSD 3-Clause License | ||
| * | ||
| * File 'README.licenses' in the root directory of this distribution contains | ||
| * full conditions and disclaimers for each license. | ||
| */ | ||
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| #include "AS_global.H" | ||
| #include "ovStore.H" | ||
| #include "splitToWords.H" | ||
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| #include <vector> | ||
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| using namespace std; | ||
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| int | ||
| main(int argc, char **argv) { | ||
| bool asCoords = true; | ||
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| char *outName = NULL; | ||
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| vector<char *> files; | ||
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| int32 arg = 1; | ||
| int32 err = 0; | ||
| while (arg < argc) { | ||
| if (strcmp(argv[arg], "-o") == 0) { | ||
| outName = argv[++arg]; | ||
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| } else if (AS_UTL_fileExists(argv[arg])) { | ||
| files.push_back(argv[arg]); | ||
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| } else { | ||
| fprintf(stderr, "ERROR: invalid arg '%s'\n", argv[arg]); | ||
| err++; | ||
| } | ||
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| arg++; | ||
| } | ||
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| if ((err) || (files.size() == 0)) { | ||
| fprintf(stderr, "usage: %s [options] file.mhap[.gz]\n", argv[0]); | ||
| fprintf(stderr, "\n"); | ||
| fprintf(stderr, " Converts mhap native output to ovb\n"); | ||
| fprintf(stderr, "\n"); | ||
| fprintf(stderr, " -o out.ovb output file\n"); | ||
| fprintf(stderr, "\n"); | ||
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| if (files.size() == 0) | ||
| fprintf(stderr, "ERROR: no overlap files supplied\n"); | ||
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| exit(1); | ||
| } | ||
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| char *ovStr = new char [1024]; | ||
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| ovOverlap ov(NULL); | ||
| ovFile *of = new ovFile(outName, ovFileFullWrite); | ||
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| for (uint32 ff=0; ff<files.size(); ff++) { | ||
| compressedFileReader *in = new compressedFileReader(files[ff]); | ||
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| // $1 $2 $3 $4 $5 $6 $7 $8 $9 $10 $11 $12 $13 | ||
| // 0 1 2 3 4 5 6 7 8 9 10 11 12 | ||
| // 0f1bd7b6-a7f2-4bcb-8575-d617f1394b8a_Basecall_2D_2d 8189 1310 8014 + b74d9367-f45a-4684-8bfc-ff533629b030_Basecall_2D_2d 14205 7340 14051 277 6711 255 cm:i:32 | ||
| // 0f1bd7b6-a7f2-4bcb-8575-d617f1394b8a_Basecall_2D_2d 8189 1152 7272 - a3026aca-57a7-4639-96bf-b76624cf2d34_Basecall_2D_2d 7731 1642 7547 157 6120 255 cm:i:24 | ||
| // aiid alen bgn end bori biid blen bgn end #match minimizers alnlen ? cm:i:errori | ||
| // | ||
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| while (fgets(ovStr, 1024, in->file()) != NULL) { | ||
| splitToWords W(ovStr); | ||
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| ov.a_iid = W(0); | ||
| ov.b_iid = W(5); | ||
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| if (ov.a_iid == ov.b_iid) | ||
| continue; | ||
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| ov.dat.ovl.forUTG = true; | ||
| ov.dat.ovl.forOBT = true; | ||
| ov.dat.ovl.forDUP = true; | ||
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| ov.dat.ovl.ahg5 = W(2); | ||
| ov.dat.ovl.ahg3 = W(1) - W(3); | ||
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| if (W[4][0] == '+') { | ||
| ov.dat.ovl.bhg5 = W(7); | ||
| ov.dat.ovl.bhg3 = W(6) - W(8); | ||
| ov.flipped(false); | ||
| } else { | ||
| ov.dat.ovl.bhg3 = W(7); | ||
| ov.dat.ovl.bhg5 = W(6) - W(8); | ||
| ov.flipped(true); | ||
| } | ||
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| ov.erate(1-((double)W(9)/W(10))); | ||
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| of->writeOverlap(&ov); | ||
| } | ||
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| arg++; | ||
| } | ||
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| delete of; | ||
| delete [] ovStr; | ||
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| exit(0); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,19 @@ | ||
| # If 'make' isn't run from the root directory, we need to set these to | ||
| # point to the upper level build directory. | ||
| ifeq "$(strip ${BUILD_DIR})" "" | ||
| BUILD_DIR := ../$(OSTYPE)-$(MACHINETYPE)/obj | ||
| endif | ||
| ifeq "$(strip ${TARGET_DIR})" "" | ||
| TARGET_DIR := ../$(OSTYPE)-$(MACHINETYPE)/bin | ||
| endif | ||
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| TARGET := mmapConvert | ||
| SOURCES := mmapConvert.C | ||
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| SRC_INCDIRS := .. ../AS_UTL ../stores liboverlap | ||
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| TGT_LDFLAGS := -L${TARGET_DIR} | ||
| TGT_LDLIBS := -lcanu | ||
| TGT_PREREQS := libcanu.a | ||
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| SUBMAKEFILES := |
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