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Xenome classify hang patch #21

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Xenome classify hang patch #21

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b23ef5b
Workaround for the xenome classify hangs problem. This does not fix t…
kathryn-beal Jun 5, 2018
e3db629
Merge pull request #1 from cancerit/feature/xenome_classify_fix
AndyMenzies Jun 5, 2018
92dc395
Merge branch 'release/1.0.0'
kathryn-beal Jun 5, 2018
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132 changes: 77 additions & 55 deletions src/GossCmdGroupReads.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ namespace // anonymous
friend class ReadClassItr;

public:

class ReadClassItr
{
public:
Expand Down Expand Up @@ -162,7 +162,7 @@ namespace // anonymous
}
}
}

if (good)
{
// cerr << "write\n";
Expand Down Expand Up @@ -195,7 +195,7 @@ namespace // anonymous
}

private:

static uint64_t pack(uint64_t pReadNum, uint8_t pClass)
{
return pReadNum << 4 | pClass;
Expand Down Expand Up @@ -238,7 +238,7 @@ namespace // anonymous
bool mDone;
};

class KmerSrc
class KmerSrc
{
public:
virtual bool valid() const = 0;
Expand Down Expand Up @@ -355,7 +355,7 @@ namespace // anonymous
mClassWriter(mNum, pBlrg);
}

Pair(uint64_t pK, uint64_t pNum, GossReadPtr pRead1, GossReadPtr pRead2, vector<Outs>& pOutputs,
Pair(uint64_t pK, uint64_t pNum, GossReadPtr pRead1, GossReadPtr pRead2, vector<Outs>& pOutputs,
ReadClassWriter& pClassWriter)
: mK(pK), mNum(pNum), mRead1(pRead1), mRead2(pRead2),
mItr1(*mRead1, mK), mItr2(*mRead2, mK),
Expand Down Expand Up @@ -546,7 +546,7 @@ namespace // anonymous
return ss.str();
}

string
string
neither(const string& pPrefix, const string& pSuffix, const string pHalf="")
{
return filename(pPrefix, pSuffix, pHalf, "neither");
Expand Down Expand Up @@ -576,7 +576,7 @@ namespace // anonymous
return filename(pPrefix, pSuffix, pHalf, pName.size() ? pName : "host");
}

void classReads(Logger& pLog, FileFactory& pFac, const string& pIn, uint64_t pNumPasses,
void classReads(Logger& pLog, FileFactory& pFac, const string& pIn, uint64_t pNumPasses,
uint64_t pNumThreads, const ReadItems& pReadItems, bool pNoWrite,
ReadClassWriter& pClassWriter, uint64_t pK, vector<uint64_t>& pCounts,
const string& pPrefix, const string& pLhsName, const string& pRhsName, const string& pSuffix)
Expand Down Expand Up @@ -685,7 +685,7 @@ namespace // anonymous
}
}

void classPairs(Logger& pLog, FileFactory& pFac, const string& pIn, uint64_t pNumPasses,
void classPairs(Logger& pLog, FileFactory& pFac, const string& pIn, uint64_t pNumPasses,
uint64_t pNumThreads, const ReadItems& pReadItems, bool pNoWrite,
ReadClassWriter& pClassWriter, uint64_t pK, vector<uint64_t>& pCounts,
const string& pPrefix, const string& pLhsName, const string& pRhsName, const string& pSuffix)
Expand All @@ -695,7 +695,7 @@ namespace // anonymous
mutex lhsM;
mutex rhsM;
mutex ambiguousM;
FileFactory::OutHolderPtr neitherP_1, neitherP_2, bothP_1, bothP_2,
FileFactory::OutHolderPtr neitherP_1, neitherP_2, bothP_1, bothP_2,
ambiguousP_1, ambiguousP_2, lhsP_1, lhsP_2, rhsP_1, rhsP_2;
vector<Outs> outs;

Expand Down Expand Up @@ -806,6 +806,53 @@ namespace // anonymous
}
}

void printStats(vector<uint64_t> counts, bool mDontWriteReads, const string& mLhsName, const string& mRhsName)
{
uint64_t total = 0;
for (uint64_t i = 0; i < counts.size(); ++i)
{
total += counts[i];
}

const uint64_t graftC = counts[0x4] + counts[0x5] + counts[0xc] + counts[0xd];
const uint64_t hostC = counts[0x2] + counts[0x3] + counts[0xa] + counts[0xb];
const uint64_t bothC = counts[0x1] + counts[0x8] + counts[0x9];
const uint64_t neitherC = counts[0x0];
const uint64_t ambigC = counts[0x6] + counts[0x7] + counts[0xe] + counts[0xf];

if (mDontWriteReads)
{
cout << 100.0 * graftC / total << '\t'
<< 100.0 * hostC / total << '\t'
<< 100.0 * bothC / total << '\t'
<< 100.0 * neitherC / total << '\t'
<< 100.0 * ambigC / total << '\n';
}
else
{
cout << "Statistics\n";
cout << "B\tG\tH\tM\t" << "count\t" << "percent\t" << "class\n";
for (uint64_t i = 0; i < counts.size(); ++i)
{
cout << (i & 8 ? '1' : '0') << '\t';
cout << (i & 4 ? '1' : '0') << '\t';
cout << (i & 2 ? '1' : '0') << '\t';
cout << (i & 1 ? '1' : '0') << '\t';
cout << counts[i] << '\t';
cout << (100.0 * double(counts[i]) / total) << '\t';
cout << '"' << classStr(mLhsName, mRhsName, i) << '"' << '\n';
}

cout << "\nSummary\n";
cout << "count\t" << "percent\t" << "class\n";
cout << graftC << '\t' << 100.0 * graftC / total << '\t' << mLhsName << '\n';
cout << hostC << '\t' << 100.0 * hostC / total << '\t' << mRhsName << '\n';
cout << bothC << '\t' << 100.0 * bothC / total << '\t' << "both" << '\n';
cout << neitherC << '\t'<< 100.0 * neitherC / total << '\t' << "neither" << '\n';
cout << ambigC << '\t' << 100.0 * ambigC / total << '\t' << "ambiguous" << '\n';
}
}

} // namespace anonymous

void
Expand Down Expand Up @@ -833,7 +880,7 @@ GossCmdGroupReads::operator()(const GossCmdContext& pCxt)
const uint64_t refB = kmersB + lhsB + rhsB;
numPasses = refB / maxB + 1;
}
log(info, "performing " + lexical_cast<string>(numPasses) +
log(info, "performing " + lexical_cast<string>(numPasses) +
" pass" + (numPasses > 1 ? "es" : ""));

fac.populate(numPasses == 1);
Expand Down Expand Up @@ -868,6 +915,9 @@ GossCmdGroupReads::operator()(const GossCmdContext& pCxt)
&umon, &log);
classPairs(log, fac, mIn, numPasses, T, items, mDontWriteReads,
classWriter, K, counts, mPrefix, mLhsName, mRhsName, "txt");
printStats(counts, mDontWriteReads, mLhsName, mRhsName);
log(info, "total elapsed time: " + lexical_cast<string>(t.check()));
exit(0);
}

if (!mFastas.empty())
Expand All @@ -886,6 +936,9 @@ GossCmdGroupReads::operator()(const GossCmdContext& pCxt)
&umon, &log);
classPairs(log, fac, mIn, numPasses, T, items, mDontWriteReads,
classWriter, K, counts, mPrefix, mLhsName, mRhsName, "fasta");
printStats(counts, mDontWriteReads, mLhsName, mRhsName);
log(info, "total elapsed time: " + lexical_cast<string>(t.check()));
exit(0);
}

if (!mFastqs.empty())
Expand All @@ -904,6 +957,9 @@ GossCmdGroupReads::operator()(const GossCmdContext& pCxt)
&umon, &log);
classPairs(log, fac, mIn, numPasses, T, items, mDontWriteReads,
classWriter, K, counts, mPrefix, mLhsName, mRhsName, "fastq");
printStats(counts, mDontWriteReads, mLhsName, mRhsName);
log(info, "total elapsed time: " + lexical_cast<string>(t.check()));
exit(0);
}
}
else
Expand All @@ -924,6 +980,9 @@ GossCmdGroupReads::operator()(const GossCmdContext& pCxt)
&umon, &log);
classReads(log, fac, mIn, numPasses, T, items, mDontWriteReads,
classWriter, K, counts, mPrefix, mLhsName, mRhsName, "txt");
printStats(counts, mDontWriteReads, mLhsName, mRhsName);
log(info, "total elapsed time: " + lexical_cast<string>(t.check()));
exit(0);
}

if (!mFastas.empty())
Expand All @@ -942,6 +1001,9 @@ GossCmdGroupReads::operator()(const GossCmdContext& pCxt)
&umon, &log);
classReads(log, fac, mIn, numPasses, T, items, mDontWriteReads,
classWriter, K, counts, mPrefix, mLhsName, mRhsName, "fasta");
printStats(counts, mDontWriteReads, mLhsName, mRhsName);
log(info, "total elapsed time: " + lexical_cast<string>(t.check()));
exit(0);
}

if (!mFastqs.empty())
Expand All @@ -960,53 +1022,13 @@ GossCmdGroupReads::operator()(const GossCmdContext& pCxt)
&umon, &log);
classReads(log, fac, mIn, numPasses, T, items, mDontWriteReads,
classWriter, K, counts, mPrefix, mLhsName, mRhsName, "fastq");
printStats(counts, mDontWriteReads, mLhsName, mRhsName);
log(info, "total elapsed time: " + lexical_cast<string>(t.check()));
exit(0);
}
}

uint64_t total = 0;
for (uint64_t i = 0; i < counts.size(); ++i)
{
total += counts[i];
}

const uint64_t graftC = counts[0x4] + counts[0x5] + counts[0xc] + counts[0xd];
const uint64_t hostC = counts[0x2] + counts[0x3] + counts[0xa] + counts[0xb];
const uint64_t bothC = counts[0x1] + counts[0x8] + counts[0x9];
const uint64_t neitherC = counts[0x0];
const uint64_t ambigC = counts[0x6] + counts[0x7] + counts[0xe] + counts[0xf];

if (mDontWriteReads)
{
cout << 100.0 * graftC / total << '\t'
<< 100.0 * hostC / total << '\t'
<< 100.0 * bothC / total << '\t'
<< 100.0 * neitherC / total << '\t'
<< 100.0 * ambigC / total << '\n';
}
else
{
cout << "Statistics\n";
cout << "B\tG\tH\tM\t" << "count\t" << "percent\t" << "class\n";
for (uint64_t i = 0; i < counts.size(); ++i)
{
cout << (i & 8 ? '1' : '0') << '\t';
cout << (i & 4 ? '1' : '0') << '\t';
cout << (i & 2 ? '1' : '0') << '\t';
cout << (i & 1 ? '1' : '0') << '\t';
cout << counts[i] << '\t';
cout << (100.0 * double(counts[i]) / total) << '\t';
cout << '"' << classStr(mLhsName, mRhsName, i) << '"' << '\n';
}

cout << "\nSummary\n";
cout << "count\t" << "percent\t" << "class\n";
cout << graftC << '\t' << 100.0 * graftC / total << '\t' << mLhsName << '\n';
cout << hostC << '\t' << 100.0 * hostC / total << '\t' << mRhsName << '\n';
cout << bothC << '\t' << 100.0 * bothC / total << '\t' << "both" << '\n';
cout << neitherC << '\t'<< 100.0 * neitherC / total << '\t' << "neither" << '\n';
cout << ambigC << '\t' << 100.0 * ambigC / total << '\t' << "ambiguous" << '\n';
}

printStats(counts, mDontWriteReads, mLhsName, mRhsName);
log(info, "total elapsed time: " + lexical_cast<string>(t.check()));
}

Expand Down Expand Up @@ -1055,7 +1077,7 @@ GossCmdFactoryGroupReads::create(App& pApp, const boost::program_options::variab

chk.throwIfNecessary(pApp);

return GossCmdPtr(new GossCmdGroupReads(in, fastas, fastqs, lines, pairs, M, T,
return GossCmdPtr(new GossCmdGroupReads(in, fastas, fastqs, lines, pairs, M, T,
lhsName, rhsName, prefix, noOut, ord));
}

Expand Down