From bcc7bacba1afa7859d7a79cb011eea7451306396 Mon Sep 17 00:00:00 2001 From: asivache Date: Thu, 4 Jun 2009 16:25:14 +0000 Subject: [PATCH] added List getTranscripts(); also more comments added git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@894 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/refdata/rodRefSeq.java | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java index f7101e89d..ba69d729b 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java @@ -52,7 +52,8 @@ public class rodRefSeq extends BasicReferenceOrderedDatum { /** Returns true if the current position this ROD is associated with is within the coding interval for at least * one of the annotated transcripts. NOTE: "coding" interval is defined as a single genomic interval, so it * does not include the UTRs of the outermost exons, but it includes introns between exons spliced into a - * transcript, or internal exons that are not spliced into a given transcript. @see isExon(). + * transcript, or internal exons that are not spliced into a given transcript. To check that a position is + * indeed within an exon but not in UTR, use isExon() && isCoding(). @see isExon(). * @return */ public boolean isCoding() { @@ -76,6 +77,15 @@ public class rodRefSeq extends BasicReferenceOrderedDatum { return false; } + /** Returns all annotated transcripts overlapping with the current position as an immutable list. + * "Overlap" is defined as position being within genomic interval corresponding to the whole + * transcript start/transcript stop coordinates, thus the position can be still in a UTR, in intron, or + * in an internal exon that is actually not spliced into the specific transcript. Use isExon(), isCoding() of + * this ROD class, or query individual Transcript objects returned by this method to get more details. + * @return + */ + public List getTranscripts() { return Collections.unmodifiableList(records) ; } + @Override public String repl() { throw new StingException("repl() is not implemented yet");