zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Make sure we always write at least 1000 points per base in each cycle's scatterplot. Print the disagreement rate between Bustard and FourBaseRecaller. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@375 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-13 00:49:41 +00:00
parent 1fb16d54e0
commit c51f51f255
1 changed files with 12 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java
View File

@ -11,6 +11,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.playground.illumina.FirecrestFileParser;
import org.broadinstitute.sting.playground.illumina.FirecrestReadData;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import java.io.File;
@ -139,6 +140,9 @@ public class FourBaseRecaller extends CommandLineProgram {
ffp = new FirecrestFileParser(DIR.getParentFile(), LANE);
fread = ffp.next();
int[][] base_counts = new int[4][bread.getFirstReadSequence().length()];
int bases_incorrect = 0, bases_total = 0;
if (debugout != null) { debugout.println("cycle int_a int_c int_g int_t bustard_base kiran_base bustard_prob kiran_prob"); }
queryid = 0;
@ -163,10 +167,14 @@ public class FourBaseRecaller extends CommandLineProgram {
bestqual[cycle] = fp.qualAtRank(0);
nextbestqual[cycle] = QualityUtils.baseAndProbToCompressedQuality(fp.indexAtRank(1), fp.probAtRank(1));
if (debugout != null && queryid < 5000 && bases.charAt(cycle) != '.') {
if (debugout != null && bases.charAt(cycle) != '.' && base_counts[BaseUtils.simpleBaseToBaseIndex(bases.charAt(cycle))][cycle] < 1000) {
debugout.println(cycle + " " + fourintensity[0] + " " + fourintensity[1] + " " + fourintensity[2] + " " + fourintensity[3] + " " + (bases.charAt(cycle)) + " " + ((char) asciiseq[cycle]) + " " + bestqual[cycle] + " " + quals[cycle]);
//System.out.println(cycle + " " + fourintensity[0] + " " + fourintensity[1] + " " + fourintensity[2] + " " + fourintensity[3] + " " + (bases.charAt(cycle)) + " " + ((char) asciiseq[cycle]) + " " + bestqual[cycle] + " " + quals[cycle]);
base_counts[BaseUtils.simpleBaseToBaseIndex(bases.charAt(cycle))][cycle]++;
}
bases_incorrect += (bases.charAt(cycle) == (char) asciiseq[cycle]) ? 0 : 1;
bases_total++;
}
sfw.addAlignment(constructSAMRecord("KIR_", new String(asciiseq), bestqual, nextbestqual, bread, sfh));
@ -180,6 +188,8 @@ public class FourBaseRecaller extends CommandLineProgram {
}
sfw.close();
System.out.println("Nonmatch rate: " + ((double) bases_incorrect)/((double) bases_total));
return 0;
}