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

Now only prints 1 warning message about duplicate headers in simpleMerge

This commit is contained in:
Mark DePristo 2011-08-29 14:41:29 -04:00
parent 61633c95a8
commit 3b09d42ed6
1 changed files with 22 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

28
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
View File

@ -116,10 +116,26 @@ public class VCFUtils {
return fields;
}
/** Only displays a warning if a logger is provided and an identical warning hasn't been already issued */
private static final class HeaderConflictWarner {
Logger logger;
Set<String> alreadyIssued = new HashSet<String>();
private HeaderConflictWarner(final Logger logger) {
this.logger = logger;
}
public void warn(final VCFHeaderLine line, final String msg) {
if ( logger != null && ! alreadyIssued.contains(line.getKey()) ) {
alreadyIssued.add(line.getKey());
logger.warn(msg);
}
}
}
public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, Logger logger) throws IllegalStateException {
HashMap<String, VCFHeaderLine> map = new HashMap<String, VCFHeaderLine>(); // from KEY.NAME -> line
HeaderConflictWarner conflictWarner = new HeaderConflictWarner(logger);
// todo -- needs to remove all version headers from sources and add its own VCF version line
for ( VCFHeader source : headers ) {
@ -152,24 +168,24 @@ public class VCFUtils {
// number, then this value should be 1. However, if the INFO field describes a pair
// of numbers, then this value should be 2 and so on. If the number of possible
// values varies, is unknown, or is unbounded, then this value should be '.'.
if ( logger != null ) logger.warn("Promoting header field Number to . due to number differences in header lines: " + line + " " + other);
conflictWarner.warn(line, "Promoting header field Number to . due to number differences in header lines: " + line + " " + other);
compOther.setNumberToUnbounded();
} else if ( compLine.getType() == VCFHeaderLineType.Integer && compOther.getType() == VCFHeaderLineType.Float ) {
// promote key to Float
if ( logger != null ) logger.warn("Promoting Integer to Float in header: " + compOther);
conflictWarner.warn(line, "Promoting Integer to Float in header: " + compOther);
map.put(key, compOther);
} else if ( compLine.getType() == VCFHeaderLineType.Float && compOther.getType() == VCFHeaderLineType.Integer ) {
// promote key to Float
if ( logger != null ) logger.warn("Promoting Integer to Float in header: " + compOther);
conflictWarner.warn(line, "Promoting Integer to Float in header: " + compOther);
} else {
throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other );
}
}
if ( ! compLine.getDescription().equals(compOther) )
if ( logger != null ) logger.warn("Allowing unequal description fields through: keeping " + compOther + " excluding " + compLine);
conflictWarner.warn(line, "Allowing unequal description fields through: keeping " + compOther + " excluding " + compLine);
} else {
// we are not equal, but we're not anything special either
if ( logger != null ) logger.warn("Ignoring header line already in map: this header line = " + line + " already present header = " + other);
conflictWarner.warn(line, "Ignoring header line already in map: this header line = " + line + " already present header = " + other);
}
} else {
map.put(key, line);