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NM attribute changed in sam jdk (?) from Integer to Short, or maybe it is presented differently by the reader depending on whether SAM or BAM is processed; in any case, both Integer and Short are safe now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1522 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-03 19:03:32 +00:00
parent ada4c5a13c
commit 5202d959bf
1 changed files with 14 additions and 5 deletions
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19
java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java
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@ -8,6 +8,7 @@ import java.util.Map.Entry;
import org.broadinstitute.sting.playground.utils.GenomicMap; import org.broadinstitute.sting.playground.utils.GenomicMap;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.AlignmentUtils;
import net.sf.picard.cmdline.CommandLineProgram; import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Option; import net.sf.picard.cmdline.Option;
@ -126,7 +127,7 @@ public class RemapAlignments extends CommandLineProgram {
badRecords++; badRecords++;
continue; continue;
} }
if ( read.getReadUnmappedFlag() ) totalUnmappedReads++; if ( AlignmentUtils.isReadUnmapped(read) ) totalUnmappedReads++;
else { else {
// destroy mate pair mapping information, if any (we will need to reconstitute pairs after remapping both ends): // destroy mate pair mapping information, if any (we will need to reconstitute pairs after remapping both ends):
read.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX); read.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
@ -218,7 +219,10 @@ public class RemapAlignments extends CommandLineProgram {
if ( attr == null ) { if ( attr == null ) {
return; // can not recompute qualities! return; // can not recompute qualities!
} }
int nm = (Integer)attr; int nm;
if ( attr instanceof Short ) nm = ((Short)attr).intValue();
else if ( attr instanceof Integer ) nm = ((Integer)attr).intValue();
else throw new RuntimeException("NM attribute is neither Short nor Integer, don't know what to do.");
if ( nm < minNM ) { if ( nm < minNM ) {
minNM = nm; minNM = nm;
cnt = 1; cnt = 1;
@ -230,12 +234,17 @@ public class RemapAlignments extends CommandLineProgram {
int cnt2 = reads.size() - cnt; // count of inferior alignments int cnt2 = reads.size() - cnt; // count of inferior alignments
r.setAttribute("X0", new Integer(cnt)); r.setAttribute("X0", new Integer(cnt));
r.setAttribute("X1", new Integer(cnt2)); r.setAttribute("X1", new Integer(cnt2));
if ( cnt2 > 255 ) cnt2 = 255; // otherwise we will be out of bounds in g_log_n if ( cnt2 > 255 ) cnt2 = 255; // otherwise we will be out of bounds in g_log_n
if ( ((Integer)r.getAttribute("NM")).intValue() == minNM ) { int nm_attr;
Object attr = r.getAttribute("NM");
if ( attr instanceof Short ) nm_attr = ((Short)attr).intValue();
else if ( attr instanceof Integer ) nm_attr = ((Integer)attr).intValue();
else throw new RuntimeException("NM attribute is neither Short nor Integer, don't know what to do.");
if ( nm_attr == minNM ) {
// one of the best alignments: // one of the best alignments: