1 files changed, 0 insertions, 85 deletions
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch
deleted file mode 100644
index 38664aeee989..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-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());