From e6cab1c6baa63cb440d86027ec00d2aee61e44b7 Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Mon, 20 Jan 2014 13:27:31 -0500
Subject: [PATCH] [BUG] change getField() logic in GffRecord
---
.../FileRecordTools/Records/GffRecord.cpp | 37 +++++++++++++++++++
src/utils/FileRecordTools/Records/GffRecord.h | 3 +-
2 files changed, 39 insertions(+), 1 deletion(-)
diff --git a/src/utils/FileRecordTools/Records/GffRecord.cpp b/src/utils/FileRecordTools/Records/GffRecord.cpp
index f13c8fd8..a91ce159 100644
--- a/src/utils/FileRecordTools/Records/GffRecord.cpp
+++ b/src/utils/FileRecordTools/Records/GffRecord.cpp
@@ -120,3 +120,40 @@ void GffRecord::printNull(QuickString &outBuf) const
}
}
+const QuickString &GffRecord::getField(int fieldNum) const
+{
+ if (fieldNum == 9 && _numFields == 9) {
+ return _group;
+ }
+ switch (fieldNum) {
+ case 1:
+ return _chrName;
+ break;
+ case 2:
+ return _source;
+ break;
+ case 3:
+ return _name;
+ break;
+ case 4:
+ return _startPosStr;
+ break;
+ case 5:
+ return _endPosStr;
+ break;
+ case 6:
+ return _score;
+ break;
+ case 7:
+ return _strand;
+ break;
+ case 8:
+ return _frame;
+ break;
+ default:
+ return Bed6Interval::getField(fieldNum);
+ break;
+ }
+}
+
+
diff --git a/src/utils/FileRecordTools/Records/GffRecord.h b/src/utils/FileRecordTools/Records/GffRecord.h
index 195d4bea..b84d96a7 100644
--- a/src/utils/FileRecordTools/Records/GffRecord.h
+++ b/src/utils/FileRecordTools/Records/GffRecord.h
@@ -27,9 +27,10 @@ public:
virtual const QuickString &getSource() const { return _source; }
virtual const QuickString &getFrame() const { return _frame; }
virtual const QuickString &getGroup() const { return _group; }
- virtual const int getNumFields() const { return _numFields; }
+ virtual int getNumFields() const { return _numFields; }
virtual void setNumFields(int val) { _numFields = val; }
+ virtual const QuickString &getField(int fieldNum) const;
//Note: using the assignment operator in a GffRecord can potentially be a performance hit,
//if the number of fields frequently differ between this object and the one being copied.
const GffRecord &operator=(const GffRecord &other);
--
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