fix CpG methyl status in figure.

lancelothk · Jul 26, 2015 · 67f9c5a · 67f9c5a
1 parent 16a055b
commit 67f9c5a
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Showing 2 changed files with 2 additions and 5 deletions.
diff --git a/BSPAT/src/edu/cwru/cbc/BSPAT/core/DrawPattern.java b/BSPAT/src/edu/cwru/cbc/BSPAT/core/DrawPattern.java
@@ -102,9 +102,6 @@ public void drawPattern(PatternLink patternLink) throws IOException {
 
 		if (patternLink.getPatternType().equals(PatternLink.METHYLATION)) {
 			int startPos = statList.get(0).getPosition() < 0 ? 0 : statList.get(0).getPosition();
-			int endPos = statList.get(statList.size() - 1)
-					.getPosition() == targetLength - 1 ? targetLength - 1 : statList.get(statList.size() - 1)
-					.getPosition() + 1;
 			if (strand.equals("-")) {
 				endCoor = endCoor - startPos;
 				beginCoor = endCoor - targetLength + 1;

diff --git a/BSPAT/src/edu/cwru/cbc/BSPAT/core/ReadAnalysisResult.java b/BSPAT/src/edu/cwru/cbc/BSPAT/core/ReadAnalysisResult.java
@@ -86,11 +86,11 @@ public List<PatternResult> readPatternFile(String region, String patternType) th
 						}
 						patternResult.addCpG(cpg);
 					} else if (items[0].charAt(i) == '@') {
-						cpg = new CpGSitePattern(i, false);
+						cpg = new CpGSitePattern(i, true);
 						if (i + 1 < regionLength && items[0].charAt(i + 1) == '@') {
 							i++;
 						} else if (i == 0) {
-							cpg = new CpGSitePattern(i - 1, false);
+							cpg = new CpGSitePattern(i - 1, true);
 						}
 						patternResult.addCpG(cpg);
 					} else if (items[0].charAt(i) == 'A' || items[0].charAt(i) == 'C' || items[0].charAt(i) == 'G' ||