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Bring SAMPileupCodec into compliance with new interface. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3383 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-05-19 01:23:29 +00:00
parent 7cfb9ff3dc
commit aedb9f6734
1 changed files with 5 additions and 6 deletions
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11
java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
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@ -29,9 +29,8 @@ import org.broad.tribble.FeatureCodec;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.exception.CodecLineParsingException;
import org.broad.tribble.util.ParsingUtils; import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broad.tribble.util.LineReader;
import java.io.File;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.regex.Pattern; import java.util.regex.Pattern;
import java.util.regex.Matcher; import java.util.regex.Matcher;
@ -44,7 +43,7 @@ import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileup
* @author mhanna * @author mhanna
* @version 0.1 * @version 0.1
*/ */
public class SAMPileupCodec implements FeatureCodec { public class SAMPileupCodec implements FeatureCodec<SAMPileupFeature> {
// the number of tokens we expect to parse from a dbSNP line // the number of tokens we expect to parse from a dbSNP line
private static final int expectedTokenCount = 10; private static final int expectedTokenCount = 10;
private static final char fldDelim = '\t'; private static final char fldDelim = '\t';
@ -59,16 +58,16 @@ public class SAMPileupCodec implements FeatureCodec {
/** /**
* Return the # of header lines for this file. * Return the # of header lines for this file.
* *
* @param f the file * @param reader the line reader
* @return 0 in this case, we assume no header lines. The DbSNP file may have a * @return 0 in this case, we assume no header lines. The DbSNP file may have a
* header line beginning with '#', but we can ignore that in the decode function. * header line beginning with '#', but we can ignore that in the decode function.
*/ */
public int headerLineCount(File f) { public int readHeader(LineReader reader) {
// we don't require a header line, but it may exist. We'll deal with that above. // we don't require a header line, but it may exist. We'll deal with that above.
return 0; return 0;
} }
public Feature decode(String line) { public SAMPileupFeature decode(String line) {
// 0 1 2 3 4 5 6 7 // 0 1 2 3 4 5 6 7
//* chrX 466 T Y 170 170 88 32 ... (piles of read bases and quals follow) //* chrX 466 T Y 170 170 88 32 ... (piles of read bases and quals follow)
//* chrX 141444 * +CA/+CA 32 468 255 25 +CA * 5 2 12 6 //* chrX 141444 * +CA/+CA 32 468 255 25 +CA * 5 2 12 6