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amr_report.cpp
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// amr_report.cpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* Identification of AMR genes using BLAST and HMM search results vs. the NCBI virulence database
*
*/
#undef NDEBUG
#include "common.hpp"
#include "tsv.hpp"
using namespace Common_sp;
#include "gff.hpp"
using namespace GFF_sp;
#include "alignment.hpp"
using namespace Alignment_sp;
#include "columns.hpp"
#include "common.inc"
namespace
{
// Global
// PAR
constexpr bool useCrossOrigin = false; // GPipe: true
constexpr double frac_delta = 1e-5;
constexpr size_t domain_min = 20; // aa
bool ident_min_user = false;
bool equidistant = false;
bool cdsExist = false;
bool print_node = false;
bool print_node_raw = false;
bool reportPseudo = false;
bool parentTargetProt = true;
string input_name;
//const string stopCodonS ("[stop]");
//const string frameShiftS ("[frameshift]");
map <string/*accession*/, Vector<AmrMutation>> accession2mutations;
struct BlastRule final : Root
// PD-2310
{
// 0 <=> undefined
// 0 .. 1
double ident {0.0};
// Of alignment
double target_coverage {0.0}; // Not used
double ref_coverage {0.0};
BlastRule (double ident_arg,
double ref_coverage_arg)
: ident (ident_arg)
, ref_coverage (ref_coverage_arg)
{
QC_ASSERT (ident > 0.0);
QC_ASSERT (ident <= 1.0);
QC_ASSERT (target_coverage >= 0.0);
QC_ASSERT (target_coverage <= 1.0);
QC_ASSERT (ref_coverage > 0.0);
QC_ASSERT (ref_coverage <= 1.0);
}
BlastRule () = default;
void saveText (ostream &os) const final
{ os << ident << ' ' << ref_coverage; }
bool empty () const final
{ return ! ident; }
};
BlastRule defaultCompleteBR;
BlastRule defaultPartialBR;
struct Fam
// Table PROTEUS.VF..FAM
{
const Fam* parent {nullptr};
// Tree
string id;
string genesymbol;
string familyName;
uchar reportable {0};
// 0,1,2
// HMM
string hmm;
// May be empty()
double tc1 {NaN};
double tc2 {NaN};
// BlastRule's
BlastRule completeBR;
BlastRule partialBR;
string type;
string subtype;
string classS;
string subclass;
Fam (const string &id_arg,
const string &genesymbol_arg,
const string &hmm_arg,
double tc1_arg,
double tc2_arg,
const BlastRule &completeBR_arg,
const BlastRule &partialBR_arg,
const string &type_arg,
const string &subtype_arg,
const string &class_arg,
const string &subclass_arg,
const string &familyName_arg,
uchar reportable_arg)
: id (id_arg)
, genesymbol (genesymbol_arg)
, familyName (familyName_arg)
, reportable (reportable_arg)
, hmm (hmm_arg)
, tc1 (tc1_arg)
, tc2 (tc2_arg)
, completeBR (completeBR_arg)
, partialBR (partialBR_arg)
, type (type_arg)
, subtype (subtype_arg)
, classS (class_arg)
, subclass (subclass_arg)
{ if (genesymbol == "-")
genesymbol. clear ();
if (hmm == "-")
hmm. clear ();
QC_ASSERT (hmm. empty () == ! tc1);
QC_ASSERT (hmm. empty () == ! tc2);
//IMPLY (! hmm. empty (), tc2 > 0);
if (familyName == "NULL")
familyName. clear ();
QC_ASSERT (tc2 >= 0);
QC_ASSERT (tc2 <= tc1);
QC_ASSERT (! completeBR. empty ())
QC_ASSERT (! partialBR. empty ());
}
Fam () = default;
void saveText (ostream &os) const
{ os << hmm << " " << tc1 << " " << tc2 << " " << familyName << " " << (int) reportable; }
bool descendantOf (const Fam* ancestor) const
{ if (! ancestor)
return true;
if (this == ancestor)
return true;
if (parent)
return parent->descendantOf (ancestor);
return false;
}
const Fam* getHmmFam () const
// Return: most specific HMM
{ const Fam* f = this;
while (f && f->hmm. empty ())
f = f->parent;
return f;
}
};
map<string/*famId*/,const Fam*> famId2fam;
// Value: !nullptr
// Not delete'd
struct Batch;
struct BlastAlignment;
struct HmmAlignment
// Query: AMR HMM
{
string sseqid;
double score1 {NaN};
double score2 {NaN};
// May be different from max(Domain::score)
const Fam* fam {nullptr};
// Query
// !nullptr
//ali_from, ali_to ??
unique_ptr<const BlastAlignment> blastAl;
// (bool)get()
HmmAlignment (const string &line,
const Batch &batch);
// Update: batch.domains
void saveText (ostream &os) const
{ os << sseqid << ' ' << score1 << ' ' << score2 << ' ' << (fam ? fam->hmm : noString); }
bool good () const
{ QC_ASSERT (fam);
QC_ASSERT (! fam->hmm. empty ());
return score1 >= fam->tc1
&& score2 >= fam->tc2;
}
private:
bool betterEq (const HmmAlignment &other,
unsigned char criterion) const
// Reflexive
// For one sseqid: one HmmAlignment is better than all others
{ ASSERT (good ());
ASSERT (other. good ());
if (sseqid != other. sseqid)
return false;
switch (criterion)
{
case 0: return fam->descendantOf (other. fam);
case 1:
{
LESS_PART (other, *this, score1);
//return score2 >= other. score2; // GP-16770
LESS_PART (other, *this, fam->tc1);
if (! equidistant)
LESS_PART (*this, other, fam->id); // Tie resolution
return true;
}
default: ERROR;
}
throw logic_error ("Never call");
}
public:
bool better (const HmmAlignment &other,
unsigned char criterion) const
{ return betterEq (other, criterion)
&& ! other. betterEq (*this, criterion); }
bool better (const BlastAlignment &other) const;
typedef pair<string/*sseqid*/,string/*FAM.id*/> Pair;
struct Domain
{
double score {0};
size_t hmmLen {0};
size_t hmmStart {0};
size_t hmmStop {0};
size_t seqLen {0};
size_t seqStart {0};
size_t seqStop {0};
Domain (const string &line,
Batch &batch);
// Input: line: hmmsearch -domtable line
Domain () = default;
};
};
struct Susceptible final : Root
{
// !empty()
string genesymbol;
double cutoff;
string classS;
string subclass;
string name;
Susceptible (const string &genesymbol_arg,
double cutoff_arg,
const string &class_arg,
const string &subclass_arg,
const string &name_arg)
: genesymbol (genesymbol_arg)
, cutoff (cutoff_arg / 100.0)
, classS (class_arg)
, subclass (subclass_arg)
, name (name_arg)
{
QC_ASSERT (cutoff > 0.0);
QC_ASSERT (cutoff <= 1.0);
QC_ASSERT (! name. empty ());
QC_ASSERT (! contains (name, '\t'));
replace (name, '_', ' ');
QC_ASSERT (! contains (name, " "));
}
Susceptible () = default;
Susceptible& operator= (Susceptible&& other) = default;
void saveText (ostream &os) const final
{ os << genesymbol
<< '\t' << cutoff
<< '\t' << classS
<< '\t' << subclass
<< '\t' << name
<< endl;
}
};
map <string/*accession*/, Susceptible> accession2susceptible;
struct BlastAlignment final : Alignment
// BLASTP or BLASTX
{
// target
size_t targetAlign {0};
size_t targetAlign_aa {0};
bool partialDna {false};
bool stopCodon {false};
// Reference protein
const bool fromHmm;
string refAccession;
// empty() <=> HMM method
size_t part {1};
// >= 1
// <= parts
size_t parts {1};
// >= 1
VectorPtr<BlastAlignment> fusions;
bool fusionRedundant {false};
// Table FAM
string famId;
string gene;
// FAM.class
string resistance;
uchar reportable {0};
string classS;
string subclass;
//bool stxtyper {false};
const Fam* brFam {nullptr};
// Valid if !fromHmm and !inFam()
BlastRule completeBR;
BlastRule partialBR;
string product;
Vector<Locus> cdss;
static constexpr size_t mismatchTail_aa = 10; // PAR
const Susceptible* susceptible {nullptr};
// In accession2susceptible
// Only for the right organism
const HmmAlignment* hmmAl {nullptr};
BlastAlignment (const string &line,
bool targetProt_arg)
: Alignment (line, targetProt_arg, true)
, fromHmm (false)
{
try
{
try
{
// refName
product = rfindSplit (refName, '|');
classS = rfindSplit (refName, '|');
subclass = rfindSplit (refName, '|');
reportable = (uchar) str2<int> (rfindSplit (refName, '|'));
resistance = rfindSplit (refName, '|');
gene = rfindSplit (refName, '|'); // Reportable_vw.class
famId = rfindSplit (refName, '|'); // Reportable_vw.fam
parts = (size_t) str2<int> (rfindSplit (refName, '|'));
part = (size_t) str2<int> (rfindSplit (refName, '|'));
refAccession = rfindSplit (refName, '|');
str2<long> (refName); // gi: dummy
if (contains (refAccession, ':'))
{
QC_ASSERT (isMutationProt ());
const string geneMutation = rfindSplit (refAccession, ':');
const size_t pos = str2<size_t> (rfindSplit (refAccession, ':'));
ASSERT (refMutation. empty ());
refMutation = std::move (AmrMutation (pos, geneMutation));
QC_ASSERT (! refMutation. empty ());
refMutation. qc ();
}
}
catch (const exception &e)
{
throw runtime_error (string ("Bad AMRFinder database\n") + e. what () + "\n" + line);
}
QC_ASSERT (! refAccession. empty ());
refName = refAccession;
replace (product, '_', ' ');
replace (classS, '_', ' ');
replace (subclass, '_', ' ');
// BlastRule
// PD-2310
if (inFam ())
{
// PD-4856
ASSERT (! brFam);
// brFam
EXEC_ASSERT (brFam = getFam ());
while (brFam)
{
if (partial ())
{
#if 0
PRINT (brFam->id);
PRINT (brFam->genesymbol);
PRINT (brFam->partialBR);
PRINT (pIdentity ());
PRINT (refCoverage ());
#endif
if (passBlastRule (brFam->partialBR))
{
//cout << "match!" << endl;
break;
}
}
else
if (passBlastRule (brFam->completeBR))
{
#if 0
PRINT (brFam->id);
PRINT (brFam->genesymbol);
PRINT (brFam->completeBR);
PRINT (pIdentity ());
PRINT (refCoverage ());
#endif
break;
}
brFam = brFam->parent;
}
}
else
{
completeBR = defaultCompleteBR;
partialBR = defaultPartialBR;
}
partialDna = false;
constexpr size_t mismatchTailDna = 10; // PAR
if (! targetProt && targetEnd - targetStart >= 30) // PAR, PD-671
{
if (refStart > 0 && targetTail (true) <= mismatchTailDna) partialDna = true;
else if (refEnd < refLen && targetTail (false) <= mismatchTailDna) partialDna = true;
}
setTargetAlign ();
if (contains (targetSeq, "*"))
stopCodon = true;
IMPLY (! targetProt, (targetEnd - targetStart) % 3 == 0); // redundant ??
// PD-1280
if ( (! targetProt || targetStart < domain_min) // PD-2381
&& refStart == 0
&& charInSet (targetSeq [0], "LIV")
&& nident < targetAlign_aa
)
nident++;
if (! targetProt)
cdss. emplace_back (0, targetName, targetStart, targetEnd, targetStrand, partialDna, 0, noString, noString);
if (isMutationProt ())
if (const Vector<AmrMutation>* refMutations = findPtr (accession2mutations, refAccession))
{
if (verbose ())
cout << "AmrMutation protein found: " << refAccession << endl << line << endl;
setSeqChanges (*refMutations, 0);
if (verbose ())
cout << endl;
}
susceptible = findPtr (accession2susceptible, refAccession);
}
catch (...)
{
cout << line << endl;
throw;
}
}
BlastAlignment (const HmmAlignment& hmmAl_arg,
const BlastAlignment* best)
: fromHmm (true)
, famId (hmmAl_arg. fam->id)
, gene (hmmAl_arg. fam->id)
, product (hmmAl_arg. fam->familyName)
, hmmAl (& hmmAl_arg)
{ ASSERT (hmmAl_arg. good ());
targetName = hmmAl_arg. sseqid;
targetProt = true;
alProt = true;
if (allele ())
ERROR_MSG (famId + " " + gene);
if (best)
{
targetSeq = best->targetSeq;
targetStart = best->targetStart;
targetEnd = best->targetEnd;
targetLen = best->targetLen;
targetStrand = best->targetStrand;
refProt = true;
refName = best->refName;
refSeq = best->refSeq;
refStart = best->refStart;
refEnd = best->refEnd;
refLen = best->refLen;
alProt = true;
nident = best->nident;
targetAlign = best->targetAlign;
targetAlign_aa = best->targetAlign_aa;
refAccession = best->refAccession;
//stxtyper = best->stxtyper;
}
}
void qc () const override
{
if (! qc_on)
return;
Alignment::qc ();
if (empty ())
return;
QC_ASSERT (! famId. empty ());
QC_ASSERT (! gene. empty ());
QC_ASSERT (part >= 1);
QC_ASSERT (part <= parts);
//QC_IMPLY (part > 1, ! fusions. empty () || fusionRedundant);
QC_IMPLY (! fusions. empty (), parts >= 2);
QC_IMPLY (isMutationProt (), ! isSusceptibleProt ());
QC_IMPLY (susceptible, isSusceptibleProt ());
QC_IMPLY (isSusceptibleProt (), fusions. empty () && ! fusionRedundant);
QC_IMPLY (isMutationProt (), fusions. empty () && ! fusionRedundant);
QC_IMPLY (! fusions. empty (), fusions. size () >= 2);
QC_IMPLY (! fusions. empty (), fusions. front () == this);
QC_IMPLY (fusionRedundant, fusions. empty ());
QC_ASSERT (! product. empty ());
QC_IMPLY (! fromHmm, ! refAccession. empty ());
QC_ASSERT (refAccession. empty () == targetSeq. empty ());
QC_ASSERT (! refAccession. empty () == (bool) refLen);
QC_ASSERT (! refAccession. empty () == (bool) nident);
QC_IMPLY (refAccession. empty () && inFam (), ! getFam () -> hmm. empty ());
QC_IMPLY (targetProt, ! partialDna);
QC_ASSERT (targetAlign);
QC_IMPLY (targetProt, targetAlign == targetAlign_aa);
QC_IMPLY (! targetProt, targetAlign == 3 * targetAlign_aa);
QC_ASSERT (nident <= targetAlign_aa);
QC_IMPLY (! refAccession. empty (), targetAlign_aa <= targetSeq. size ());
QC_IMPLY (! refMutation. empty (), isMutationProt ());
#if 0
if (targetProt)
for (const Locus& cds : cdss)
QC_ASSERT ( cds. size () == 3 * targetLen + 3
|| cds. size () == 3 * targetLen
);
#endif
if (! targetProt)
{
for (const Locus& cds : cdss)
QC_ASSERT (cds. contig == targetName);
}
QC_IMPLY (! seqChanges. empty (), isMutationProt ());
QC_ASSERT ((fromHmm || inFam ()) == completeBR. empty ());
QC_ASSERT ((fromHmm || inFam ()) == partialBR. empty ());
}
void report (TsvOut &td,
const string &parentTargetName,
bool mutationAll) const
{ // PD-736, PD-774, PD-780, PD-799
const string proteinName (isMutationProt ()
? product
: susceptible
? susceptible->name
: refProtExactlyMatched (true) || parts >= 2 || refAccession. empty () // PD-3187, PD-3192
? product
: nvl (getMatchFam () -> familyName, na)
);
ASSERT (! contains (proteinName, '\t'));
Vector<Locus> cdss_ (cdss);
if (cdss_. empty ())
cdss_ << Locus ();
Vector<SeqChange> seqChanges_ (seqChanges);
if (seqChanges_. empty ())
seqChanges_ << SeqChange ();
for (const Locus& cds : cdss_)
{
if (targetProt)
{
if (parentTargetProt)
{ ASSERT (targetName == parentTargetName); }
else
if (cds. contig != parentTargetName)
continue;
}
else
{ ASSERT (targetName == parentTargetName); }
for (const SeqChange& seqChange : seqChanges_)
{
const string method (empty () ? na : getMethod (cds));
VectorPtr<AmrMutation> mutations (seqChange. mutations);
if (mutations. empty ())
mutations << nullptr;
for (const AmrMutation* mut : mutations)
{
IMPLY (! verbose (), isMutationProt () == ! (seqChange. empty () && ! mut));
const bool isMutation = ! seqChange. empty () && mut && ! seqChange. replacement;
if (mutationAll)
{
if (! isMutationProt ())
continue;
}
else if (isMutationProt () && ! isMutation)
continue;
if (! input_name. empty ())
td << input_name;;
td << (targetProt ? nvl(targetName, na) : na); // PD-2534
if (cdsExist)
td << (empty () ? na : (cds. contig. empty () ? nvl (targetName, na) : cds. contig))
<< (empty () ? 0 : (cds. contig. empty () ? targetStart : cds. start) + 1)
<< (empty () ? 0 : (cds. contig. empty () ? targetEnd : cds. stop))
<< (empty () ? na : (cds. contig. empty () ? (targetStrand ? "+" : "-") : (cds. strand ? "+" : "-")));
td << (isMutationProt ()
? mut
? seqChange. empty ()
? mut->wildtype ()
: mut->geneMutation
: gene + "_" + seqChange. getMutationStr ()
: fusion2geneSymbols ()
)
<< (isMutationProt ()
? mut
? seqChange. empty ()
? proteinName + " [WILDTYPE]"
: mut->name
: proteinName + " [UNKNOWN]"
: proteinName
)
<< (isMutationProt () || fusion2core () ? "core" : "plus"); // PD-2825
// PD-1856
if (isMutationProt ())
td << "AMR"
<< "POINT"
<< (mut ? nvl (mut->classS, na) : na)
<< (mut ? nvl (mut->subclass, na) : na);
else
td << nvl (fusion2type (), na)
<< nvl (fusion2subtype (), na)
<< nvl (fusion2class (), na)
<< nvl (fusion2subclass (), na);
td << method
<< (targetProt ? targetLen : targetAlign_aa);
if (refAccession. empty ())
td << na
<< na
<< na
<< na
<< na
<< na;
else
td << refLen
<< refCoverage () * 100.0
<< pIdentity () * 100.0 // refIdentity
<< targetSeq. size ()
<< refAccession
<< product
;
// PD-775
if (isMutationProt ())
td << na
<< na;
else
{
if (const HmmAlignment* hmmAl_ = fusion2hmmAl ())
td << hmmAl_->fam->hmm
<< hmmAl_->fam->familyName;
else
{
td << na
<< na;
ASSERT (method != "HMM");
}
}
if (cdsExist)
{
IMPLY (cds. crossOrigin, useCrossOrigin);
if (useCrossOrigin)
{
if (cds. crossOrigin)
td << cds. contigLen;
else
td << na;
}
}
if (print_node)
{
if (! print_node_raw && allele () && ! refProtExactlyMatched (true))
td << gene;
else
td << fusion2famIds ();
}
IMPLY (isMutationProt () && isMutation /*! seqChange. empty () && mut && ! seqChange. replacement*/, hasMutation ());
td. newLn ();
}
}
}
}
bool isMutationProt () const
{ return resistance == "mutation"; }
bool isSusceptibleProt () const
{ return resistance == "susceptible"; } // Similar to isMutationProt(): low identity <=> point mutations
bool inFam () const
{ return ! isMutationProt ()
&& ! isSusceptibleProt ();
}
#if 0
bool notInFam () const
{ return ! inFam (); }
#endif
Set<string> getMutationSymbols () const
{ Set<string> mutationSymbols;
for (const SeqChange& seqChange : seqChanges)
if (! seqChange. empty ())
for (const AmrMutation* mutation : seqChange. mutations)
mutationSymbols << mutation->geneMutation;
return mutationSymbols;
}
bool allele () const
{ return famId != gene && parts == 1; }
size_t refEffectiveLen () const
{ return partialDna ? refEnd - refStart : refLen; }
bool partial () const
// Requires: good()
{ return refCoverage () < defaultCompleteBR. ref_coverage - frac_delta; }
bool getTargetStrand (const Locus &cds) const
{ return targetProt
? cds. empty ()
? true
: cds. strand
: targetStrand;
}
size_t missedDnaStart (const Locus &cds) const
{ return 3 * (getTargetStrand (cds)
? refStart
: refLen - refEnd
);
}
size_t missedDnaStop (const Locus &cds) const
{ return 3 * (getTargetStrand (cds)
? refLen - refEnd
: refStart
);
}
bool truncated (const Locus &cds) const
{ return (missedDnaStart (cds) > 0 && (targetProt ? (cds. empty () ? false : cds. atContigStart ()) : targetStart <= Locus::end_delta))
|| (missedDnaStop (cds) > 0 && (targetProt ? (cds. empty () ? false : cds. atContigStop ()) : targetLen - targetEnd <= Locus::end_delta));
}
bool truncatedCds () const
{ for (const Locus& cds : cdss)
if (truncated (cds))
return true;
return false;
}
bool alleleMatch () const
{ return refProtExactlyMatched (true) && allele (); }
bool alleleReportable () const // PD-3583
{ return alleleMatch () && reportable >= 2; }
uchar getReportable () const
{ if (const Fam* f = getMatchFam ())
return f->reportable;
return 0;
}
uchar fusion2reportable () const
{ ASSERT (! isMutationProt ());
if (susceptible)
return 2;
if (fusions. empty ())
return getReportable ();
uchar reportable_max = 0;
for (const BlastAlignment* fusion : fusions)
maximize (reportable_max, fusion->getReportable ());
return reportable_max;
}
private:
string getGeneSymbol () const
{ return susceptible
? susceptible->genesymbol
: alleleMatch ()
? famId
: nvl (getMatchFam () -> genesymbol, na);
}
public:
string fusion2geneSymbols () const
{ ASSERT (! isMutationProt ());
if (fusions. empty ())
return getGeneSymbol ();
string s;
for (const BlastAlignment* fusion : fusions)
add (s, "/" /*fusion_infix*/, fusion->getGeneSymbol ()); // PD-5155 ??
return s;
}
string fusion2famIds () const
{ if (isMutationProt () || fusions. empty ())
return famId;
string s;
for (const BlastAlignment* fusion : fusions)
add (s, fusion_infix, fusion->famId);
return s;
}
private:
bool isCore () const
{ return fusion2reportable () >= 2 || alleleReportable (); }
public:
bool fusion2core () const
{ ASSERT (! isMutationProt ());
if (fusions. empty ())
return isCore ();
for (const BlastAlignment* fusion : fusions)
if (fusion->isCore ())
return true;
return false;
}
private:
string getType () const
{ return susceptible ? "AMR" : getMatchFam () -> type; }
public:
string fusion2type () const
{ ASSERT (! isMutationProt ());
if (fusions. empty ())
return getType ();
StringVector vec;
for (const BlastAlignment* fusion : fusions)
vec << fusion->getType ();
vec. sort ();
vec. uniq ();
return vec. toString ("/");
}
private:
string getSubtype () const
{ return susceptible ? "AMR" : getMatchFam () -> subtype; }
public:
string fusion2subtype () const
{ ASSERT (! isMutationProt ());
if (fusions. empty ())
return getSubtype ();
StringVector vec;
for (const BlastAlignment* fusion : fusions)
vec << fusion->getSubtype ();
vec. sort ();
vec. uniq ();
return vec. toString ("/");
}
private:
string getClass () const
{ if (alleleMatch () && ! subclass. empty ()) // class may be empty()
return classS;
return susceptible ? susceptible->classS : getMatchFam () -> classS;
}
public:
string fusion2class () const
{ ASSERT (! isMutationProt ());
if (fusions. empty ())
return getClass ();
StringVector vec;
for (const BlastAlignment* fusion : fusions)
vec << std::move (StringVector (fusion->getClass (), '/', true));
vec. sort ();
vec. uniq ();
return vec. toString ("/");
}
private:
string getSubclass () const
{ if (alleleMatch () && ! subclass. empty ())
return subclass;
return susceptible ? susceptible->subclass : getMatchFam () -> subclass;
}
public:
string fusion2subclass () const
{ ASSERT (! isMutationProt ());
if (fusions. empty ())
return getSubclass ();
StringVector vec;
for (const BlastAlignment* fusion : fusions)
vec << std::move (StringVector (fusion->getSubclass (), '/', true));
vec. sort ();
vec. uniq ();
return vec. toString ("/");
}
const HmmAlignment* fusion2hmmAl () const
{ if (fusions. empty ())
return hmmAl;
for (const BlastAlignment* fusion : fusions)
if (fusion->hmmAl)
return fusion->hmmAl;
return nullptr;
}
string getMethod (const Locus &cds) const
{ //IMPLY (refExactlyMatched () && ! mutation_all. get (), ! isMutationProt ())
string method (fromHmm
? "HMM"
: isMutationProt ()
? "POINT"
: refProtExactlyMatched (true)
? alleleMatch ()
? "ALLELE"
: "EXACT" // PD-776
: partial ()
? truncated (cds)
? "PARTIAL_CONTIG_END" // PD-2267
: "PARTIAL"
: "BLAST"
);
// PD-2088, PD-2320
bool suffix = true;
if ( ( method == "BLAST"
|| method == "PARTIAL"
|| method == "PARTIAL_CONTIG_END"
)
//&& ! targetProt
)
{
if (stopCodon)
{
method = "INTERNAL_STOP";
suffix = false;
}
#if 0
else if (frameShift)
{
method = "FRAME_SHIFT";
suffix = false;
}
#endif
}
if (suffix && method != "HMM")
method += (targetProt ? "P" : "X");
return method;
}
// PD-736
bool passBlastRule (const BlastRule &br) const
{ ASSERT (! br. empty ());
return pIdentity () >= br. ident - frac_delta
&& refCoverage () >= br. ref_coverage - frac_delta;
}
bool partialPseudo () const
{ return partial ()
&& ! cdss. empty ()
&& ! truncatedCds ();
}
bool pseudo () const
{ return stopCodon
|| partialPseudo ();
}
bool good () const
{ ASSERT (! fromHmm);
if (refAccession. empty ())
return true;
//if (! refMutation. empty ()) // PD-4981: drop
//return true;