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Ignore header line if it happens to be passed to the codec again, instead of crashing on it 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5116 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-01-28 21:44:33 +00:00
parent 8d389e149f
commit fa8963522b
1 changed files with 10 additions and 5 deletions
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15
java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafCodec.java
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@ -102,20 +102,21 @@ public class MafCodec implements FeatureCodec {
if (line.startsWith("#")) return null;
// split the line
String[] tokens = line.split("\\t");
String[] tokens = line.split("\\t",-1);
if ( expectedTokenCount == -1 ) { // do this only when we receive the first line and do not know the number of columns yet
// we have not seen a single line yet, let's initialize the number of fields from the first line:
expectedTokenCount = tokens.length;
log.info("MAF: line has "+expectedTokenCount+" fields (columns)");
if ( expectedTokenCount == 9 ) {
mafType = MAF_TYPE.LITE;
log.info("MAF file appears to be MAF Lite");
} else {
if ( expectedTokenCount == 63 ) {
if ( expectedTokenCount >= 63 ) {
mafType = MAF_TYPE.ANNOTATED;
log.info("MAF file appears to be MAF-Annotated");
} else {
log.info("MAF file has "+expectedTokenCount +" columns, unknown file type");
log.info("MAF file has "+expectedTokenCount +" columns in first line, unknown file type");
}
}
if ( line.contains("Chromosome") && line.contains("Start") && line.contains("Build")) {
@ -135,11 +136,15 @@ public class MafCodec implements FeatureCodec {
}
if (tokens.length != expectedTokenCount) {
log.error("MAF line contains wrong number of columns");
if (tokens.length < expectedTokenCount) {
log.error("MAF line contains too few columns ("+tokens.length+")");
return null;
}
if (tokens.length > expectedTokenCount) {
log.warn("MAF line contains more columns than expected ("+tokens.length+"); extra columns discarded");
}
if ( tokens[CHR_COL].equals("Chromosome") ) return null; // if someone uses this codec manually and feeds it the header line multiple times...
// create a new feature from the line:
int start = Integer.valueOf(tokens[START_COL]);