Merge remote-tracking branch 'remotes/origin/master'

Author: lh3

Makefile

@@ -18,6 +18,9 @@ SUBDIRS=	.
 ifeq ($(shell uname -s),Linux)
 	LIBS += -lrt
 endif
+ifeq ($(shell uname -s),GNU/kFreeBSD)
+	LIBS += -lrt
+endif
 
 .SUFFIXES:.c .o .cc
 

bwashm.c

@@ -9,6 +9,10 @@
 #include <stdio.h>
 #include "bwa.h"
 
+#ifndef PATH_MAX
+#  define PATH_MAX 1024
+#endif
+
 int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
 {
 	const char *name;

bwt_gen.c

@@ -876,7 +876,6 @@ static void BWTIncBuildRelativeRank(bgint_t* __restrict sortedRank, bgint_t* __r
 	bgint_t i, c;
 	bgint_t s, r;
 	bgint_t lastRank, lastIndex;
-	bgint_t oldInverseSa0RelativeRank = 0;
 	bgint_t freq;
 
 	lastIndex = numItem;
@@ -887,7 +886,6 @@ static void BWTIncBuildRelativeRank(bgint_t* __restrict sortedRank, bgint_t* __r
 	s = seq[numItem];
 	relativeRank[s] = numItem;
 	if (lastRank == oldInverseSa0) {
-		oldInverseSa0RelativeRank = numItem;
 		oldInverseSa0++;	// so that this segment of code is not run again
 		lastRank++;			// so that oldInverseSa0 become a sorted group with 1 item
 	}
@@ -920,7 +918,6 @@ static void BWTIncBuildRelativeRank(bgint_t* __restrict sortedRank, bgint_t* __r
 			lastRank = r;
 			relativeRank[s] = i;
 			if (r == oldInverseSa0) {
-				oldInverseSa0RelativeRank = i;
 				oldInverseSa0++;	// so that this segment of code is not run again
 				lastRank++;			// so that oldInverseSa0 become a sorted group with 1 item
 			}
@@ -950,15 +947,12 @@ static void BWTIncBuildBwt(unsigned int* insertBwt, const bgint_t *relativeRank,
 static void BWTIncMergeBwt(const bgint_t *sortedRank, const unsigned int* oldBwt, const unsigned int *insertBwt,
 						   unsigned int* __restrict mergedBwt, const bgint_t numOldBwt, const bgint_t numInsertBwt)
 {
-	unsigned int bitsInWordMinusBitPerChar;
 	bgint_t leftShift, rightShift;
 	bgint_t o;
 	bgint_t oIndex, iIndex, mIndex;
 	bgint_t mWord, mChar, oWord, oChar;
 	bgint_t numInsert;
 
-	bitsInWordMinusBitPerChar = BITS_IN_WORD - BIT_PER_CHAR;
-
 	oIndex = 0;
 	iIndex = 0;
 	mIndex = 0;