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Improved error reporting 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3520 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-06-09 17:52:48 +00:00
parent 4f00e265a8
commit fdded73861
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
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@ -398,7 +398,7 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
if(isProteinCodingTranscript && parsedTranscriptRod.cdsSequence.length() % 3 != 0) {
if (!isMitochondrialTranscript) {
logger.warn("WARNING: Transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. Skipping...");
logger.error("ERROR: Transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. Skipping...");
//discard transcripts where CDS length is not a multiple of 3
skippedTranscriptCounter++;
return;
@ -426,7 +426,7 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
} while( parsedTranscriptRod.cdsSequence.length() % 3 != 0);
} else {
logger.warn("WARNING: Mitochnodrial transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. The CDS does not cover the entire transcript, so its not possible to use A's from the polyA tail. Skipping...");
logger.error("ERROR: Mitochnodrial transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. The CDS does not cover the entire transcript, so its not possible to use A's from the polyA tail. Skipping...");
skippedTranscriptCounter++;
return;
}