| /dports/biology/vt/vt-0.57721/ |
| H A D | indel_genotyping_record.cpp | 392 void IndelGenotypingRecord::add_allele(double contam, int32_t allele, uint8_t mapq, bool fwd, uint3… in add_allele()
489 uint8_t mapq = bam_get_mapq(s); in process_read() local
597 uint8_t mapq = bam_get_mapq(s); in process_read() local
614 uint8_t mapq = bam_get_mapq(s); in process_read() local
722 uint8_t mapq = bam_get_mapq(s); in process_read() local
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| H A D | complex_genotyping_record.cpp | 428 void ComplexGenotypingRecord::add_allele(double contam, int32_t allele, uint8_t mapq, bool fwd, uin… in add_allele()
525 uint8_t mapq = bam_get_mapq(s); in process_read() local
633 uint8_t mapq = bam_get_mapq(s); in process_read() local
650 uint8_t mapq = bam_get_mapq(s); in process_read() local
758 uint8_t mapq = bam_get_mapq(s); in process_read() local
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| H A D | vntr_genotyping_record.cpp | 376 void VNTRGenotypingRecord::add_allele(double contam, int32_t allele, uint8_t mapq, bool fwd, uint32… in add_allele()
473 uint8_t mapq = bam_get_mapq(s); in process_read() local
570 uint8_t mapq = bam_get_mapq(s); in process_read() local
678 uint8_t mapq = bam_get_mapq(s); in process_read() local
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| H A D | snp_genotyping_record.cpp | 379 void SNPGenotypingRecord::add_allele(double contam, int32_t allele, uint8_t mapq, bool fwd, uint32_… in add_allele()
474 uint8_t mapq = bam_get_mapq(s); in process_read() local
562 uint8_t mapq = bam_get_mapq(s); in process_read() local
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| H A D | bcf_genotyping_buffered_reader.cpp | 629 uint8_t mapq = bam_get_mapq(s); in collect_sufficient_statistics() local
759 uint8_t mapq = bam_get_mapq(s); in collect_sufficient_statistics() local
894 uint8_t mapq = bam_get_mapq(s); in collect_sufficient_statistics() local
1179 uint8_t mapq = bam_get_mapq(s); in collect_sufficient_statistics() local
1463 uint8_t mapq = bam_get_mapq(s); in collect_sufficient_statistics() local
1571 uint8_t mapq = bam_get_mapq(s); in collect_sufficient_statistics() local
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| H A D | read_filter.cpp | 252 uint32_t mapq = bam_get_mapq(s); in bam_print_key_values() local
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| /dports/biology/bowtie2/bowtie2-2.4.4/ |
| H A D | unique.h | 112 virtual TMapq mapq( in mapq() function
187 virtual TMapq mapq( in mapq() function
433 virtual TMapq mapq( in mapq() function
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | unique.h | 111 virtual TMapq mapq( in mapq() function
186 virtual TMapq mapq( in mapq() function
446 virtual TMapq mapq( in mapq() function
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
| H A D | casbar_consensus_realign.h | 12 …ProfileChar(TProfileChar &profileChar, bool &top, Dna5 const &readBase, double &qual, double &mapq) in addToProfileChar()
60 …ProfileChar(TProfileChar &profileChar, bool &top, Dna5 const &readBase, double &qual, double &mapq) in removeFromProfileChar()
189 double mapq = 0; in reAlign() local
257 double mapq = fragStore.alignQualityStore[alignIt->id].score; in reAlign() local
313 double mapq = fragStore.alignQualityStore[alignIt->id].score; in reAlign() local
738 double mapq = fragStore.alignQualityStore[contigReadsIt->id].score; in reAlign() local
764 double mapq = fragStore.alignQualityStore[contigReadsIt->id].score; in reAlign() local
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| H A D | bisar.h | 202 TScore &mapq, in writeBsAlignment()
394 TScore mapq; member
435 TScore mapq; in verifyRead() local
492 computeMapq(TScore &mapq, TId &bestId, unsigned countHits, TId &secBestId, TFragmentStore &store, T… in computeMapq()
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| /dports/biology/sra-tools/sra-tools-2.11.0/test/samline/ |
| H A D | sam.py | 182 def make_prim( qname, flags, refname, refalias, pos, mapq, cigar, rnxt = "*", pnxt = "0" ) : argument
190 def make_sec( qname, flags, refname, refalias, pos, mapq, cigar, rnxt = "*", pnxt = "0" ) : argument
273 …def __init__( self, qname, flags, refname, refalias, pos, mapq, cigar, seq, rnxt, pnxt, tags="" ) : argument
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| /dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/library/ |
| H A D | FilterBamWorker.h | 94 int mapq; variable
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
| H A D | cram_samtools.c | 51 int mapq, in bam_construct_seq()
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| /dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
| H A D | cram_samtools.c | 49 int mapq, in bam_construct_seq()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
| H A D | cram_samtools.c | 49 int mapq, in bam_construct_seq()
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| /dports/biology/stacks/stacks-2.4/htslib/cram/ |
| H A D | cram_samtools.c | 49 int mapq, in bam_construct_seq()
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
| H A D | cram_samtools.c | 49 int mapq, in bam_construct_seq()
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| /dports/biology/bbmap/bbmap/current/consensus/ |
| H A D | BaseGraph.java | 107 final int mapq=(r.samline==null ? 20 : r.samline.mapq+1); in add() local
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
| H A D | sam.y | 349 int mapq; variable
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| /dports/biology/minimap2/minimap2-2.24/python/ |
| H A D | mappy.pyx | 19 …def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, tran… argument
69 def mapq(self): return self._mapq member in Alignment
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| /dports/biology/subread/subread-2.0.2-source/src/ |
| H A D | subtools.c | 198 int mapq = -1; in main() local
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/align/ |
| H A D | iterator.h | 201 int32_t mapq; member
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/align/ |
| H A D | iterator.h | 201 int32_t mapq; member
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/ |
| H A D | csamrecords.cpp | 204 …Hit( const string& qname, TFlags flags, const string& rname, TPos pos, TMapQ mapq, const TCigar& c… in InitSingleHit()
215 …Hit( const string& qname, TFlags flags, const string& rname, TPos pos, TMapQ mapq, const TCigar& c… in InitPairedHit()
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| /dports/biology/bowtie/bowtie-1.3.1/ |
| H A D | sam.cpp | 129 void SAMHitSink::append(BTString& o, const Hit& h, int mapq, int xms) { in append()
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