public static void main(String[] args) throws Exception {
NativeLibraryLoader l = new NativeLibraryLoader();
l.load("/home/lmose/code/abra/target");
NativeAssembler assem = new NativeAssembler();
assem.setTruncateOutputOnRepeat(true);
assem.setMaxContigs(5000);
assem.setMaxPathsFromRoot(5000);
assem.setKmer(new int[] {43});
assem.setReadLength(100);
assem.setMinKmerFrequency(2);
assem.setMaxAverageDepth(400);
assem.setShouldSearchForSv(true);
// String bam1 = args[0];
String bam1 = "/home/lmose/dev/abra/sv/test.bam";
List<String> inputFiles = new ArrayList<String>();
inputFiles.add(bam1);
// String output = args[2];
String output = "/home/lmose/dev/abra/sv/output.txt";
// chr18:60,793,358-60,793,758
Feature region = new Feature("chr18", 60793358, 60793758);
String prefix = "pre";
boolean checkForDupes = true;
ReAligner realigner = new ReAligner();
CompareToReference2 c2r = new CompareToReference2();
// c2r.init(args[3]);
c2r.init("/home/lmose/reference/chr18/chr18.fa");
List<Feature> regions = new ArrayList<Feature>();
regions.add(region);
String contigs =
assem.assembleContigs(
inputFiles, output, "asm_temp", regions, prefix, checkForDupes, realigner, c2r);
System.err.println(contigs);
System.err.println("-------------------------");
List<BreakpointCandidate> svCandidates = assem.getSvCandidateRegions();
for (BreakpointCandidate svCandidate : svCandidates) {
System.err.println(
"SV: " + region.getDescriptor() + "-->" + svCandidate.getRegion().getDescriptor());
}
// assem.assembleContigs(args[0], args[1], "contig");
// for (int i=0; i<10; i++) {
// run(args[0], args[1] + "_" + i);
// }
// run(args[0], args[1]);
// assem.assembleContigs("/home/lmose/code/abra/src/main/c/1810_reads.txt",
// "/home/lmose/code/abra/src/main/c/1810.fa", "bar");
}
private void evalRegion(Feature region, String regionBases) {
boolean shouldInclude = false;
NativeAssembler assembler = new NativeAssembler();
StringBuffer readBuf =
new StringBuffer((ReAligner.MAX_REGION_LENGTH + 2 * readLength) * readLength);
for (int j = 0; j <= regionBases.length() - readLength; j++) {
readBuf.append("0"); // forward strand only
String read = regionBases.substring(j, j + readLength);
readBuf.append(read);
readBuf.append(qualities);
}
String contig =
assembler.nativeAssemble(
readBuf.toString(),
region.getDescriptor(),
"eval",
0,
1,
(ReAligner.MAX_REGION_LENGTH + 2 * readLength) * 2,
readLength,
kmers,
1,
0,
.01,
1,
MAX_NODES);
int basesIdx = contig.indexOf('\n') + 1;
if (basesIdx < contig.length()) {
String contigBases = contig.substring(basesIdx, contig.length() - 1);
if (regionBases.equals(contigBases)) {
shouldInclude = true;
}
}
if (shouldInclude) {
includeRegions.add(region);
} else {
excludeRegions.add(region);
}
}