Package: bowtie / 1.2.2+dfsg-4

seqan-rename-fill-to-resize.patch Patch series | download
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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

--- bowtie.orig/diff_sample.h
+++ bowtie/diff_sample.h
@@ -457,7 +457,7 @@
 	// 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)
@@ -537,7 +537,7 @@
 		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;
@@ -661,7 +661,7 @@
 	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;
@@ -725,7 +725,7 @@
 	assert_eq(length(_doffs), d+1);
 	// Size sPrime appropriately
 	reserve(sPrime, sPrimeSz + padding, Exact()); // reserve extra slot for LS
-	fill(sPrime, sPrimeSz + padding, OFF_MASK, Exact());
+	resize(sPrime, sPrimeSz + padding, 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;
@@ -949,7 +949,7 @@
 		// arrays back into sPrime.
 		VMSG_NL("  Allocating rank array");
 		reserve(_isaPrime, length(sPrime), 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());
--- bowtie.orig/blockwise_sa.h
+++ bowtie/blockwise_sa.h
@@ -665,8 +665,8 @@
 					try {
 						// Allocate and initialize containers for holding bucket
 						// sizes and representatives.
-						fill(tparams[tid].bucketSzs, numBuckets, 0, Exact());
-						fill(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
+						resize(tparams[tid].bucketSzs, numBuckets, 0, Exact());
+						resize(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
 					} catch(bad_alloc &e) {
 						if(this->_passMemExc) {
 							throw e; // rethrow immediately
@@ -1055,7 +1055,7 @@
 				hi = _sampleSuffs[cur_block];
 				//zHi.resizeExact(_dcV);
 				//zHi.fillZero();
-				fill(zHi, _dcV, 0, Exact());
+				resize(zHi, _dcV, 0, Exact());
 				assert_eq(getValue(zHi, 0), 0);
 				calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
 			}
@@ -1066,7 +1066,7 @@
 				lo = _sampleSuffs[cur_block-1];
 				//zLo.resizeExact(_dcV);
 				//zLo.fillZero();
-				fill(zLo, _dcV, 0, Exact());
+				resize(zLo, _dcV, 0, Exact());
 				assert_gt(_dcV, 3);
 				assert_eq(getValue(zLo, 0), 0);
 				calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());