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Searched refs:countReads (Results 1 – 25 of 31) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/
H A DCountReadsIntegrationTest.java84 countReads(interval_args, "count_reads_sorted.bam", null, count); in testCountBAMReadsWithIntervals()
89 countReads(interval_args, "count_reads_sorted.cram", "count_reads.fasta", count); in testCountCRAMReadsWithIntervals()
92 …private void countReads(final String interval_args, final String fileName, final String referenceN… in countReads() method in CountReadsIntegrationTest
/dports/security/vault/vault-1.8.2/vendor/github.com/apple/foundationdb/flow/
H A DSystemMonitor.h52 int64_t countReads; member
96 countReads = getValue(LiteralStringRef("Net2.CountReads")); in init()
H A DSystemMonitor.cpp130 .detail("ReadCalls", netData.countReads - statState->networkState.countReads) in customSystemMonitor()
H A DNet2.actor.cpp207 Int64MetricHandle countReads; member in N2::sealed
330 ++g_net2->countReads; in read()
539 countReads.init(LiteralStringRef("Net2.CountReads")); in initMetrics()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/
H A DMysqlAssemblyDbi.cpp129 qint64 MysqlAssemblyDbi::countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os) { in countReads() function in U2::MysqlAssemblyDbi
135 return a->countReads(r, os); in countReads()
353 stat.readsCount = a->countReads(U2_REGION_MAX, os); in pack()
H A DMysqlAssemblyDbi.h50 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
/dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/debug_messages_translation/
H A DAssemblyMessageTranslator.cpp63 const qint64 countOfReads = dbi->countReads(assemblyId, wholeAssembly, os); in getTranslation()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/util/
H A DAssemblyAdapter.h51 virtual qint64 countReads(const U2Region &r, U2OpStatus &os) = 0;
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/assembly/
H A DRTreeAssemblyAdapter.h39 virtual qint64 countReads(const U2Region &r, U2OpStatus &os);
H A DSingleTableAssemblyAdapter.cpp109 qint64 SingleTableAssemblyAdapter::countReads(const U2Region &r, U2OpStatus &os) { in countReads() function in U2::SingleTableAssemblyAdapter
121 return countReads(r, os); in countReadsPrecise()
H A DSingleTableAssemblyAdapter.h39 virtual qint64 countReads(const U2Region &r, U2OpStatus &os);
H A DMultiTableAssemblyAdapter.h53 virtual qint64 countReads(const U2Region &r, U2OpStatus &os);
H A DMultiTableAssemblyAdapter.cpp251 qint64 MultiTableAssemblyAdapter::countReads(const U2Region &r, U2OpStatus &os) { in countReads() function in U2::MultiTableAssemblyAdapter
258 int n = a->singleTableAdapter->countReads(r, os); in countReads()
727 qint64 nReadsTotal = multiTableAdapter->countReads(U2_REGION_MAX, os); in migrateAll()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/
H A DU2AssemblyDbi.h115 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os) = 0;
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/
H A DMysqlSingleTableAssemblyAdapter.h43 virtual qint64 countReads(const U2Region &r, U2OpStatus &os);
H A DMysqlSingleTableAssemblyAdapter.cpp118 qint64 MysqlSingleTableAssemblyAdapter::countReads(const U2Region &r, U2OpStatus &os) { in countReads() function in U2::MysqlSingleTableAssemblyAdapter
131 return countReads(r, os); in countReadsPrecise()
H A DMysqlMultiTableAssemblyAdapter.h54 virtual qint64 countReads(const U2Region &region, U2OpStatus &os);
H A DMysqlMultiTableAssemblyAdapter.cpp111 qint64 MysqlMultiTableAssemblyAdapter::countReads(const U2Region &r, U2OpStatus &os) { in countReads() function in U2::MysqlMultiTableAssemblyAdapter
119 int n = a->singleTableAdapter->countReads(r, os); in countReads()
722 qint64 nReadsTotal = multiTableAdapter->countReads(U2_REGION_MAX, os); in migrateAll()
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/assembly/
H A DAssemblyDbiUnitTests.cpp161 qint64 numReads = assemblyDbi->countReads(id, U2_REGION_MAX, os); in Test()
168 qint64 numReads = assemblyDbi->countReads(id, testRegion, os); in Test()
180 qint64 val = assemblyDbi->countReads(id, U2_REGION_MAX, os); in Test()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/
H A DSQLiteAssemblyDbi.h48 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
H A DSQLiteAssemblyDbi.cpp125 qint64 SQLiteAssemblyDbi::countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os)… in countReads() function in U2::SQLiteAssemblyDbi
131 return a->countReads(r, os); in countReads()
323 stat.readsCount = a->countReads(U2_REGION_MAX, os); in pack()
/dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/
H A DDbi.h142 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
H A DSamtoolsBasedDbi.h107 virtual qint64 countReads(const U2DataId &assemblyId, const U2Region &r, U2OpStatus &os);
/dports/biology/ugene/ugene-40.1/src/plugins/genome_aligner/src/
H A DGenomeAlignerIO.cpp166 readsInAssembly = rDbi->countReads(assembly.id, wholeAssembly, status); in GenomeAlignerDbiReader()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/gobjects/
H A DAssemblyObject.cpp159 qint64 readsCount = srcAssemblyDbi->countReads(srcObjId, desiredRegion, os); in dbi2dbiExtractRegion()

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