gentoo-overlay/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch

Description: Renamed seqan::fill function calls to use seqan::resize.
 SeqAn 1.3 renamed seqan::fill() to seqan::resize().
 SeqAn ticket: http://trac.seqan.de/ticket/77
Forwarded: no
Author: Ognyan Kulev <ogi@debian.org>
Last-Update: 2014-08-13

--- a/blockwise_sa.h
+++ b/blockwise_sa.h
@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS
 		try {
 			// Allocate and initialize containers for holding bucket
 			// sizes and representatives.
-			fill(bucketSzs, numBuckets, 0, Exact());
-			fill(bucketReps, numBuckets, OFF_MASK, Exact());
+			resize(bucketSzs, numBuckets, 0, Exact());
+			resize(bucketReps, numBuckets, OFF_MASK, Exact());
 		} catch(bad_alloc &e) {
 			if(this->_passMemExc) {
 				throw e; // rethrow immediately
@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
 				// Not the last bucket
 				assert_lt(_cur, length(_sampleSuffs));
 				hi = _sampleSuffs[_cur];
-				fill(zHi, _dcV, 0, Exact());
+				resize(zHi, _dcV, 0, Exact());
 				assert_eq(zHi[0], 0);
 				calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
 			}
@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
 				assert_gt(_cur, 0);
 				assert_leq(_cur, length(_sampleSuffs));
 				lo = _sampleSuffs[_cur-1];
-				fill(zLo, _dcV, 0, Exact());
+				resize(zLo, _dcV, 0, Exact());
 				assert_gt(_dcV, 3);
 				assert_eq(zLo[0], 0);
 				calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
--- a/diff_sample.h
+++ b/diff_sample.h
@@ -452,7 +452,7 @@ static String<T> getDeltaMap(T v, const
 	// Declare anchor-map-related items
 	String<T> amap;
 	size_t amapEnts = 1;
-	fill(amap, v, 0xffffffff, Exact());
+	resize(amap, v, 0xffffffff, Exact());
 	amap[0] = 0;
 	// Print out difference cover (and optionally calculate
 	// anchor map)
@@ -532,7 +532,7 @@ public:
 		assert_gt(_d, 0);
 		assert_eq(1, popCount(_v)); // must be power of 2
 		// Build map from d's to idx's
-		fill(_dInv, _v, 0xffffffff, Exact());
+		resize(_dInv, _v, 0xffffffff, Exact());
 		uint32_t lim = (uint32_t)length(_ds);
 		for(uint32_t i = 0; i < lim; i++) {
 			_dInv[_ds[i]] = i;
@@ -656,7 +656,7 @@ void DifferenceCoverSample<TStr>::doBuil
 	VMSG_NL("  Doing sanity check");
 	TIndexOffU added = 0;
 	String<TIndexOffU> sorted;
-	fill(sorted, length(_isaPrime), OFF_MASK, Exact());
+	resize(sorted, length(_isaPrime), OFF_MASK, Exact());
 	for(size_t di = 0; di < this->d(); di++) {
 		uint32_t d = _ds[di];
 		size_t i = 0;
@@ -717,7 +717,7 @@ void DifferenceCoverSample<TStr>::buildS
 	assert_eq(length(_doffs), d+1);
 	// Size sPrime appropriately
 	reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS
-	fill(sPrime, sPrimeSz, OFF_MASK, Exact());
+	resize(sPrime, sPrimeSz, OFF_MASK, Exact());
 	// Slot suffixes from text into sPrime according to the mu
 	// mapping; where the mapping would leave a blank, insert a 0
 	TIndexOffU added = 0;
@@ -823,7 +823,7 @@ void DifferenceCoverSample<TStr>::build(
 		// arrays back into sPrime.
 		VMSG_NL("  Allocating rank array");
 		reserve(_isaPrime, length(sPrime)+1, Exact());
-		fill(_isaPrime, length(sPrime), OFF_MASK, Exact());
+		resize(_isaPrime, length(sPrime), OFF_MASK, Exact());
 		assert_gt(length(_isaPrime), 0);
 		{
 			Timer timer(cout, "  Ranking v-sort output time: ", this->verbose());