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No longer enforce MAX_ALLELE_SIZE in VCF codec 

-- Instead issue a warning when a large (>1MB) record is encountered
-- Optimized ref.getBytes()[i] => (byte)ref.charAt(i), which avoids an implicit O(n) allocation each iteration through computeReverseClipping()
This commit is contained in:
Mark DePristo 2012-01-17 21:06:02 -05:00
parent 0c7865fdb5
commit 763c81d520
1 changed files with 6 additions and 5 deletions
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11
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -18,7 +18,7 @@ import java.util.zip.GZIPInputStream;
public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
public final static int MAX_EXPLICIT_ALLELE_SIZE = (int)Math.pow(2, 16);
public final static int MAX_ALLELE_SIZE_BEFORE_WARNING = (int)Math.pow(2, 20);
protected final static Logger log = Logger.getLogger(VCFCodec.class);
protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column
@ -522,8 +522,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
if ( allele == null || allele.length() == 0 )
generateException("Empty alleles are not permitted in VCF records", lineNo);
if ( MAX_EXPLICIT_ALLELE_SIZE != -1 && allele.length() > MAX_EXPLICIT_ALLELE_SIZE )
generateException(String.format("Allele detected with length %d, exceeding max size %d. Please remove this from the VCF file before continuing", allele.length(), MAX_EXPLICIT_ALLELE_SIZE), lineNo);
if ( MAX_ALLELE_SIZE_BEFORE_WARNING != -1 && allele.length() > MAX_ALLELE_SIZE_BEFORE_WARNING )
log.warn(String.format("Allele detected with length %d exceeding max size %d at approximately line %d, likely resulting in degraded VCF processing performance", allele.length(), MAX_ALLELE_SIZE_BEFORE_WARNING, lineNo));
if ( isSymbolicAllele(allele) ) {
if ( isRef ) {
@ -576,12 +576,13 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
public static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
boolean clipping = true;
final byte ref0 = (byte)ref.charAt(0);
for ( Allele a : unclippedAlleles ) {
if ( a.isSymbolic() )
continue;
if ( a.length() < 1 || (a.getBases()[0] != ref.getBytes()[0]) ) {
if ( a.length() < 1 || (a.getBases()[0] != ref0) ) {
clipping = false;
break;
}
@ -608,7 +609,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
stillClipping = false;
else if ( ref.length() == clipping )
generateException("bad alleles encountered", lineNo);
else if ( a.getBases()[a.length()-clipping-1] != ref.getBytes()[ref.length()-clipping-1] )
else if ( a.getBases()[a.length()-clipping-1] != ((byte)ref.charAt(ref.length()-clipping-1)) )
stillClipping = false;
}
if ( stillClipping )