Changes to RELEASE_HISTORY and VERSION and chmods

RELEASE_HISTORY

-Version 2.8.0 (July-05-2010)
+Version 2.8.2 (July-18-2010)
+1. Fixed a bug in bedFile.h preventing GFF strands from being read properly.
+2. Fixed a bug in intersectBed that occasionally caused spurious overlaps between BAM alignments and BED features.
+3. Fixed bug in intersectBed causing -r to not report the same result when files are swapped.
+4. Added checks to groupBy to prevent the selection of improper opCols and groups.
+5. Fixed various compilation issues, esp. for groupBy, bedToBam, and bedToIgv.
+6. Updated the usage statements to reflect bed/gff/vcf support.
+7. Added new fileType functions for auto-detecting gzipped or regular files.  Thanks to Assaf Gordon.
+
+
+Version 2.8.1 (July-05-2010)
 1.  Added bedToIgv.
 
 

src/bed12ToBed6/Makefile

@@ -35,6 +35,7 @@ $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
 			
 clean:
 	@echo "Cleaning up."

src/bedToBam/Makefile

@@ -37,7 +37,8 @@ $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-			
+	@$(MAKE)  -C $(UTILITIES_DIR)/fileType/
+				
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*

src/bedToIgv/Makefile

@@ -36,7 +36,8 @@ $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-			
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
+				
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*

src/closestBed/Makefile

@@ -32,6 +32,7 @@ $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
 
 clean:
 	@echo "Cleaning up."