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Update BCF2 to put PASS as offset 0 not at the end 

-- Unfortunately this commit breaks backward compatibility with all existing BCF2 files...
This commit is contained in:
Mark DePristo 2012-08-01 17:09:22 -04:00
parent 25c773ef33
commit c3c3d18611
4 changed files with 6 additions and 10 deletions
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2
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
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@ -202,7 +202,7 @@ public final class BCF2Decoder {
return null; return null;
else { else {
final String s = new String(bytes, 0, goodLength); final String s = new String(bytes, 0, goodLength);
return BCF2Utils.isCollapsedString(s) ? BCF2Utils.exploreStringList(s) : s; return BCF2Utils.isCollapsedString(s) ? BCF2Utils.explodeStringList(s) : s;
} }
} catch ( IOException e ) { } catch ( IOException e ) {
throw new ReviewedStingException("readByte failure", e); throw new ReviewedStingException("readByte failure", e);

10
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
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@ -79,23 +79,19 @@ public final class BCF2Utils {
final Set<String> seen = new HashSet<String>(); final Set<String> seen = new HashSet<String>();
final ArrayList<String> dict = new ArrayList<String>(); final ArrayList<String> dict = new ArrayList<String>();
boolean sawPASS = false; dict.add(VCFConstants.PASSES_FILTERS_v4); // special case the special PASS field
// set up the strings dictionary // set up the strings dictionary
for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) { for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
if ( line instanceof VCFIDHeaderLine && ! (line instanceof VCFContigHeaderLine) ) { if ( line instanceof VCFIDHeaderLine && ! (line instanceof VCFContigHeaderLine) ) {
final VCFIDHeaderLine idLine = (VCFIDHeaderLine)line; final VCFIDHeaderLine idLine = (VCFIDHeaderLine)line;
if ( ! seen.contains(idLine.getID())) { if ( ! seen.contains(idLine.getID())) {
sawPASS = sawPASS || idLine.getID().equals(VCFConstants.PASSES_FILTERS_v4);
dict.add(idLine.getID()); dict.add(idLine.getID());
seen.add(idLine.getID()); seen.add(idLine.getID());
} }
} }
} }
if ( ! sawPASS )
dict.add(VCFConstants.PASSES_FILTERS_v4); // special case the special PASS field
return dict; return dict;
} }
@ -177,7 +173,7 @@ public final class BCF2Utils {
*/ */
@Requires({"collapsed != null", "isCollapsedString(collapsed)"}) @Requires({"collapsed != null", "isCollapsedString(collapsed)"})
@Ensures("result != null") @Ensures("result != null")
public static final List<String> exploreStringList(final String collapsed) { public static final List<String> explodeStringList(final String collapsed) {
assert isCollapsedString(collapsed); assert isCollapsedString(collapsed);
final String[] exploded = collapsed.substring(1).split(","); final String[] exploded = collapsed.substring(1).split(",");
return Arrays.asList(exploded); return Arrays.asList(exploded);

2
public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java
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@ -351,7 +351,7 @@ public class BCF2EncoderDecoderUnitTest extends BaseTest {
public void testEncodingListOfString(List<String> strings, String expected) throws IOException { public void testEncodingListOfString(List<String> strings, String expected) throws IOException {
final String collapsed = BCF2Utils.collapseStringList(strings); final String collapsed = BCF2Utils.collapseStringList(strings);
Assert.assertEquals(collapsed, expected); Assert.assertEquals(collapsed, expected);
Assert.assertEquals(BCF2Utils.exploreStringList(collapsed), strings); Assert.assertEquals(BCF2Utils.explodeStringList(collapsed), strings);
} }
// ----------------------------------------------------------------- // -----------------------------------------------------------------

2
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
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@ -77,7 +77,7 @@ public class VCFIntegrationTest extends WalkerTest {
String testVCF = privateTestDir + "ex2.vcf"; String testVCF = privateTestDir + "ex2.vcf";
String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s "; String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF; String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("a04a0fc22fedb516c663e56e51fc1e27")); WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e8f721ce81e4fdadba13c5291027057f"));
executeTest("Test writing samtools WEx BCF example", spec1); executeTest("Test writing samtools WEx BCF example", spec1);
} }