From 9b177c573fd22b0ca7bcffc5c68609e891199aeb Mon Sep 17 00:00:00 2001
From: BenLangmead <langmea@cs.jhu.edu>
Date: Thu, 8 Jun 2017 16:05:43 -0400
Subject: [PATCH] fix failure to fully sort diff cov sample

---
 multikey_qsort.h | 96 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 48 insertions(+), 48 deletions(-)

diff --git a/multikey_qsort.h b/multikey_qsort.h
index d3deb8e..18936de 100644
--- a/multikey_qsort.h
+++ b/multikey_qsort.h
@@ -475,9 +475,9 @@ void mkeyQSortSuf(
 }
 
 struct QSortRange {
-        size_t begin;
-        size_t end;
-        size_t depth;
+	size_t begin;
+	size_t end;
+	size_t depth;
 };
 
 template<typename T>
@@ -494,29 +494,29 @@ void mkeyQSortSuf2(
 	size_t upto = OFF_MASK,
 	std::vector<size_t>* boundaries = NULL)
 {
-        std::vector<std::vector<QSortRange> > block_list;
+	std::vector<std::vector<QSortRange> > block_list;
 	while(true) {
-                size_t begin = 0, end = 0, depth = 0;
+		size_t begin = 0, end = 0, depth = 0;
 		if(block_list.size() == 0) {
-	                begin = _begin;
+			begin = _begin;
 			end = _end;
 			depth = _depth;
 		} else {
-	                if(block_list.back().size() > 0) {
-		                begin = block_list.back()[0].begin;
+			if(block_list.back().size() > 0) {
+				begin = block_list.back()[0].begin;
 				end = block_list.back()[0].end;
 				depth = block_list.back()[0].depth;
 				block_list.back().erase((block_list.back()).begin());
 			} else {
-		                block_list.resize(block_list.size() - 1);
+				block_list.resize(block_list.size() - 1);
 				if(block_list.size() == 0) {
-			                break;
+					break;
 				}
 			}
 		}
 		if(depth == upto) {
-	                if(boundaries != NULL) {
-		                (*boundaries).push_back(end);
+			if(boundaries != NULL) {
+				(*boundaries).push_back(end);
 			}
 			continue;
 		}
@@ -525,19 +525,19 @@ void mkeyQSortSuf2(
 		size_t a, b, c, d, /*e,*/ r;
 		size_t n = end - begin;
 		if(n <= 1) { // 1-element list already sorted
-	          if(n == 1 && boundaries != NULL) {
-		          boundaries->push_back(end);
-		  }
-		  continue;
+			if(n == 1 && boundaries != NULL) {
+				boundaries->push_back(end);
+			}
+			continue;
 		}
 		CHOOSE_AND_SWAP_PIVOT(SWAP2, CHAR_AT_SUF); // pick pivot, swap it into [begin]
 		int v = CHAR_AT_SUF(begin, depth); // v <- randomly-selected pivot value
 #ifndef NDEBUG
 		{
-	                bool stillInBounds = false;
+			bool stillInBounds = false;
 			for(size_t i = begin; i < end; i++) {
-		                if(depth < (hlen-s[i])) {
-			                stillInBounds = true;
+				if(depth < (hlen-s[i])) {
+					stillInBounds = true;
 					break;
 				} else { /* already fell off this suffix */ }
 			}
@@ -547,29 +547,29 @@ void mkeyQSortSuf2(
 		a = b = begin;
 		c = d = /*e =*/ end-1;
 		while(true) {
-	          // Invariant: everything before a is = pivot, everything
-	          // between a and b is <
-	          int bc = 0; // shouldn't have to init but gcc on Mac complains
-		  while(b <= c && v >= (bc = CHAR_AT_SUF(b, depth))) {
-		          if(v == bc) {
-			          SWAP2(s, s2, a, b); a++;
-			  }
-			  b++;
-		  }
-		  // Invariant: everything after d is = pivot, everything
-		  // between c and d is >
-		  int cc = 0; // shouldn't have to init but gcc on Mac complains
-		  while(b <= c && v <= (cc = CHAR_AT_SUF(c, depth))) {
-		          if(v == cc) {
-			          SWAP2(s, s2, c, d); d--; /*e--;*/
-			  }
-			  //else if(c == e && v == hi) e--;
-			  c--;
-		  }
-		  if(b > c) break;
-		  SWAP2(s, s2, b, c);
-		  b++;
-		  c--;
+			// Invariant: everything before a is = pivot, everything
+			// between a and b is <
+			int bc = 0; // shouldn't have to init but gcc on Mac complains
+			while(b <= c && v >= (bc = CHAR_AT_SUF(b, depth))) {
+			if(v == bc) {
+				SWAP2(s, s2, a, b); a++;
+			}
+			b++;
+		}
+		// Invariant: everything after d is = pivot, everything
+		// between c and d is >
+		int cc = 0; // shouldn't have to init but gcc on Mac complains
+		while(b <= c && v <= (cc = CHAR_AT_SUF(c, depth))) {
+			if(v == cc) {
+				SWAP2(s, s2, c, d); d--; /*e--;*/
+			}
+			//else if(c == e && v == hi) e--;
+			c--;
+		}
+		if(b > c) break;
+			SWAP2(s, s2, b, c);
+			b++;
+			c--;
 		}
 		assert(a > begin || c < end-1);                      // there was at least one =s
 		assert_lt(/*e*/d-c, n); // they can't all have been > pivot
@@ -583,7 +583,7 @@ void mkeyQSortSuf2(
 		block_list.push_back(tmp1);
 		block_list.back().clear();
 		if(r > 0) { // recurse on <'s
-	                QSortRange tmp2;
+			QSortRange tmp2;
 			block_list.back().push_back(tmp2);
 			block_list.back().back().begin = begin;
 			block_list.back().back().end = begin + r;
@@ -591,16 +591,16 @@ void mkeyQSortSuf2(
 		}
 		// Do not recurse on ='s if the pivot was the off-the-end value;
 		// they're already fully sorted
-		if(v != hi) { // recurse on ='s
-	                QSortRange tmp3;
+		//if(v != hi) { // recurse on ='s
+			QSortRange tmp3;
 			block_list.back().push_back(tmp3);
 			block_list.back().back().begin = begin + r;
 			block_list.back().back().end = begin + r + (a-begin) + (end-d-1);
 			block_list.back().back().depth = depth + 1;
-		}
+			//}
 		r = d-c;   // r <- # of >'s excluding those exhausted
-		if(r > 0 && v < hi-1) { // recurse on >'s
-	                QSortRange tmp4;
+		if(r > 0 /*&& v < hi-1*/) { // recurse on >'s
+			QSortRange tmp4;
 			block_list.back().push_back(tmp4);
 			block_list.back().back().begin = end - r;
 			block_list.back().back().end = end;