diff options
Diffstat (limited to 'sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch')
| -rw-r--r-- | sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch | 85 |
1 files changed, 85 insertions, 0 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 new file mode 100644 index 000000000000..38664aeee989 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch @@ -0,0 +1,85 @@ +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()); |