Merge pull request #39 from satta/gcc-issue

move around to_cigar_int
mengyao · Aug 19, 2016 · fb2e302 · fb2e302
2 parents c216584 + c341ce2
commit fb2e302
Show file tree

Hide file tree

Showing 3 changed files with 34 additions and 28 deletions.
diff --git a/src/Makefile b/src/Makefile
@@ -1,6 +1,6 @@
 CC = gcc
 CXX = g++
-CFLAGS := -Wall -pipe -O3
+CFLAGS := -Wall -pipe -O2
 CXXFLAGS := $(CFLAGS)
 LOBJS = ssw.o
 LCPPOBJS = ssw_cpp.o

diff --git a/src/ssw.c b/src/ssw.c
@@ -529,6 +529,37 @@ static alignment_end* sw_sse2_word (const int8_t* ref,
 	return bests;
 }
 
+/*!     @function               Produce CIGAR 32-bit unsigned integer from CIGAR operation and CIGAR length
+        @param  length          length of CIGAR
+        @param  op_letter       CIGAR operation character ('M', 'I', etc)
+        @return                 32-bit unsigned integer, representing encoded CIGAR operation and length
+*/
+uint32_t to_cigar_int (uint32_t length, char op_letter)
+{
+        switch (op_letter) {
+                case 'M': /* alignment match (can be a sequence match or mismatch */
+                default:
+                        return length << BAM_CIGAR_SHIFT;
+                case 'S': /* soft clipping (clipped sequences present in SEQ) */
+                        return (length << BAM_CIGAR_SHIFT) | (4u);
+                case 'D': /* deletion from the reference */
+                        return (length << BAM_CIGAR_SHIFT) | (2u);
+                case 'I': /* insertion to the reference */
+                        return (length << BAM_CIGAR_SHIFT) | (1u);
+                case 'H': /* hard clipping (clipped sequences NOT present in SEQ) */
+                        return (length << BAM_CIGAR_SHIFT) | (5u);
+                case 'N': /* skipped region from the reference */
+                        return (length << BAM_CIGAR_SHIFT) | (3u);
+                case 'P': /* padding (silent deletion from padded reference) */
+                        return (length << BAM_CIGAR_SHIFT) | (6u);
+                case '=': /* sequence match */
+                        return (length << BAM_CIGAR_SHIFT) | (7u);
+                case 'X': /* sequence mismatch */
+                        return (length << BAM_CIGAR_SHIFT) | (8u);
+        }
+        return (uint32_t)-1; // This never happens
+}
+
 static cigar* banded_sw (const int8_t* ref,
 				 const int8_t* read,
 				 int32_t refLen,

diff --git a/src/ssw.h b/src/ssw.h
@@ -22,7 +22,7 @@ extern "C" {
 
 #define MAPSTR "MIDNSHP=X"
 #ifndef BAM_CIGAR_SHIFT
-#define BAM_CIGAR_SHIFT 4
+#define BAM_CIGAR_SHIFT 4u
 #endif
 
 
@@ -159,32 +159,7 @@ int32_t mark_mismatch (int32_t ref_begin1,
 	@param	op_letter	CIGAR operation character ('M', 'I', etc)
 	@return			32-bit unsigned integer, representing encoded CIGAR operation and length
 */
-static inline uint32_t to_cigar_int (uint32_t length, char op_letter)
-{
-	switch (op_letter) {
-		case 'M': /* alignment match (can be a sequence match or mismatch */
-		default:
-			return length << BAM_CIGAR_SHIFT;
-		case 'S': /* soft clipping (clipped sequences present in SEQ) */
-			return (length << BAM_CIGAR_SHIFT) | (4u);
-		case 'D': /* deletion from the reference */
-			return (length << BAM_CIGAR_SHIFT) | (2u);
-		case 'I': /* insertion to the reference */
-			return (length << BAM_CIGAR_SHIFT) | (1u);
-		case 'H': /* hard clipping (clipped sequences NOT present in SEQ) */
-			return (length << BAM_CIGAR_SHIFT) | (5u);
-		case 'N': /* skipped region from the reference */
-			return (length << BAM_CIGAR_SHIFT) | (3u);
-		case 'P': /* padding (silent deletion from padded reference) */
-			return (length << BAM_CIGAR_SHIFT) | (6u);
-		case '=': /* sequence match */
-			return (length << BAM_CIGAR_SHIFT) | (7u);
-		case 'X': /* sequence mismatch */
-			return (length << BAM_CIGAR_SHIFT) | (8u);
-	}
-	return (uint32_t)-1; // This never happens
-}
-
+uint32_t to_cigar_int (uint32_t length, char op_letter);
 
 /*!	@function		Extract CIGAR operation character from CIGAR 32-bit unsigned integer
 	@param	cigar_int	32-bit unsigned integer, representing encoded CIGAR operation and length