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tlemanetlemane
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fix howdesbt query
1 parent 25bf19e commit f71599c

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15 files changed

+1837
-1607
lines changed

15 files changed

+1837
-1607
lines changed

‎km_howdesbt/bloom_filter.cc‎

Lines changed: 106 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,98 @@ using std::endl;
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#define u32 std::uint32_t
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#define u64 std::uint64_t
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//----------
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//
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// debugging defines--
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//
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// In "normal" builds, the triggering defines here are *not* #defined, so that
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// no run-time penalty is incurred.
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//
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//----------
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//#define bloom_filter_supportDebug // if this is #defined, extra code is added
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// .. to allow debugging prints to be
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// .. turned on and off;
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#ifndef bloom_filter_supportDebug
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#define dbgAdd_dump_pos_with_mer ;
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#define dbgAdd_dump_h_pos_with_mer ;
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#define dbgAdd_dump_pos ;
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#define dbgAdd_dump_h_pos ;
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#define dbgContains_dump_pos_with_mer ;
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#define dbgContains_dump_h_pos_with_mer ;
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#define dbgContains_dump_pos ;
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#define dbgContains_dump_h_pos ;
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#define dbgLookup_determined_brief1 ;
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#define dbgLookup_determined_brief2 ;
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#define dbgAdjust_pos_list1 ;
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#define dbgAdjust_pos_list2 ;
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#define dbgRestore_pos_list1 ;
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#define dbgRestore_pos_list2 ;
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#endif // not bloom_filter_supportDebug
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#ifdef bloom_filter_supportDebug
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#define dbgAdd_dump_pos_with_mer \
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if (dbgAdd) cerr << mer << " write " << pos << endl;
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#define dbgAdd_dump_h_pos_with_mer \
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if (dbgAdd) cerr << mer << " write" << h << " " << pos << endl;
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#define dbgAdd_dump_pos \
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if (dbgAdd) cerr << "write " << pos << endl;
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#define dbgAdd_dump_h_pos \
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if (dbgAdd) cerr << "write" << h << " " << pos << endl;
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#define dbgContains_dump_pos_with_mer \
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if (dbgContains) cerr << mer << " read " << pos << endl;
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#define dbgContains_dump_h_pos_with_mer \
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if (dbgContains) cerr << mer << " read" << h << " " << pos << endl;
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#define dbgContains_dump_pos \
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if (dbgContains) cerr << "read " << pos << endl;
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#define dbgContains_dump_h_pos \
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if (dbgContains) cerr << "read" << h << " " << pos << endl;
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#define dbgLookup_determined_brief1 \
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{ \
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if (dbgRankSelectLookup) \
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cerr << " DeterminedBriefFilter::lookup(" << pos << ")" << endl; \
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if (dbgRankSelectLookup) \
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{ \
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if ((*bvDet)[pos] == 0) \
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cerr << " bvDet[" << pos << "] == 0 --> unresolved" << endl;\
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else \
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cerr << " bvDet[" << pos << "] == 1" << endl; \
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} \
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}
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#define dbgLookup_determined_brief2 \
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if (dbgRankSelectLookup) \
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cerr << " bvHow[" << howPos << "] == " << (*bvHow)[howPos] \
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<< " --> " << (((*bvHow)[howPos]==1)?"present":"absent") \
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<< endl;
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#define dbgAdjust_pos_list1 \
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if (dbgAdjustPosList) \
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cerr << " adjust_positions_in_list(" << numUnresolved << ")" << endl;
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#define dbgAdjust_pos_list2 \
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if (dbgAdjustPosList) \
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cerr << " " << pos << " --> " << (pos-rank) << endl;
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#define dbgRestore_pos_list1 \
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if (dbgAdjustPosList) \
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cerr << " restore_positions_in_list(" << numUnresolved << ")" << endl;
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#define dbgRestore_pos_list2 \
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if (dbgAdjustPosList) \
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cerr << " " << pos << " --> " << kmerPositions[posIx] << endl;
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#endif // bloom_filter_supportDebug
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//----------
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//
@@ -889,6 +981,7 @@ void BloomFilter::add
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if (pos < numBits)
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{
891983
(*bv).write_bit(pos);
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dbgAdd_dump_pos_with_mer;
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}
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894987
if (numHashes > 1)
@@ -901,6 +994,7 @@ void BloomFilter::add
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if (pos < numBits)
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{
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(*bv).write_bit(pos); // $$$ MULTI_VECTOR write each bit to a different vector
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dbgAdd_dump_h_pos_with_mer;
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}
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}
9061000
}
@@ -916,6 +1010,7 @@ void BloomFilter::add
9161010
if (pos < numBits)
9171011
{
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(*bv).write_bit(pos);
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dbgAdd_dump_pos;
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}
9201015

9211016
if (numHashes > 1)
@@ -928,6 +1023,7 @@ void BloomFilter::add
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if (pos < numBits)
9291024
{
9301025
(*bv).write_bit(pos); // $$$ MULTI_VECTOR write each bit to a different vector
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dbgAdd_dump_h_pos;
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}
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}
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}
@@ -949,6 +1045,7 @@ bool BloomFilter::contains
9491045
u64 pos = h1 % hashModulus;
9501046
if (pos < numBits)
9511047
{
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dbgContains_dump_pos_with_mer;
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if ((*bv)[pos] == 0) return false;
9531050
}
9541051

@@ -961,6 +1058,7 @@ bool BloomFilter::contains
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pos = hashValues[h] % hashModulus;
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if (pos < numBits)
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{
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dbgContains_dump_h_pos_with_mer;
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if ((*bv)[pos] == 0) return false; // $$$ MULTI_VECTOR read each bit from a different vector
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}
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}
@@ -978,6 +1076,7 @@ bool BloomFilter::contains
9781076
u64 pos = h1 % hashModulus;
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if (pos < numBits)
9801078
{
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dbgContains_dump_pos;
9811080
if ((*bv)[pos] == 0) return false;
9821081
}
9831082

@@ -990,6 +1089,7 @@ bool BloomFilter::contains
9901089
pos = hashValues[h] % hashModulus;
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if (pos < numBits)
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{
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dbgContains_dump_h_pos;
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if ((*bv)[pos] == 0) return false; // $$$ MULTI_VECTOR read each bit from a different vector
9941094
}
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}
@@ -1198,10 +1298,12 @@ int DeterminedBriefFilter::lookup
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// we assume, without checking, that 0 <= pos < numBits
11991299

12001300
BitVector* bvDet = bvs[0];
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dbgLookup_determined_brief1;
12011302
if ((*bvDet)[pos] == 0) return unresolved;
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12031304
BitVector* bvHow = bvs[1];
12041305
u64 howPos = bvDet->rank1(pos);
1306+
dbgLookup_determined_brief2;
12051307
if ((*bvHow)[howPos] == 1) return present;
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else return absent;
12071309
}
@@ -1211,12 +1313,14 @@ void DeterminedBriefFilter::adjust_positions_in_list
12111313
u64 numUnresolved)
12121314
{
12131315
BitVector* bvDet = bvs[0];
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dbgAdjust_pos_list1;
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12151318
for (u64 posIx=0 ; posIx<numUnresolved ; posIx++)
12161319
{
12171320
u64 pos = kmerPositions[posIx];
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u64 rank = bvDet->rank1(pos);
12191322
kmerPositions[posIx] = pos - rank; // $$$ isn't this just rank0(pos)?
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dbgAdjust_pos_list2;
12201324
}
12211325
}
12221326

@@ -1225,11 +1329,13 @@ void DeterminedBriefFilter::restore_positions_in_list
12251329
u64 numUnresolved)
12261330
{
12271331
BitVector* bvDet = bvs[0];
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dbgRestore_pos_list1;
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12291334
for (u64 posIx=0 ; posIx<numUnresolved ; posIx++)
12301335
{
12311336
u64 pos = kmerPositions[posIx];
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kmerPositions[posIx] = bvDet->select0(pos);
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dbgRestore_pos_list2;
12331339
}
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}
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