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tobiasrauschtobiasrausch
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fix const
1 parent accc3c8 commit 1b40aa2

13 files changed

+46
-50
lines changed

‎src/asmode.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -93,7 +93,7 @@ namespace torali {
9393
uint32_t sp = 0; // sequence pointer
9494

9595
// Parse the CIGAR
96-
uint32_t* cigar = bam_get_cigar(rec);
96+
const uint32_t* cigar = bam_get_cigar(rec);
9797
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {
9898
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF)) {
9999
sp += bam_cigar_oplen(cigar[i]);
@@ -229,7 +229,7 @@ namespace torali {
229229
// Get sequence
230230
std::string sequence;
231231
sequence.resize(rec->core.l_qseq);
232-
uint8_t* seqptr = bam_get_seq(rec);
232+
const uint8_t* seqptr = bam_get_seq(rec);
233233
for (int i = 0; i < rec->core.l_qseq; ++i) sequence[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
234234
int32_t readlen = sequence.size();
235235

‎src/assemble.h

+7-7
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@ namespace torali
2323

2424
template<typename TAlign>
2525
inline void
26-
convertAlignment(std::string const& query, TAlign& align, EdlibAlignMode const modeCode, EdlibAlignResult& cigar) {
26+
convertAlignment(std::string const& query, TAlign& align, EdlibAlignMode const modeCode, EdlibAlignResult const& cigar) {
2727
// Input alignment
2828
TAlign alignIn;
2929
alignIn.resize(boost::extents[align.shape()[0]][align.shape()[1]]);
@@ -88,7 +88,7 @@ namespace torali
8888
}
8989

9090
inline void
91-
buildSuperstring(std::string const& seqI, std::string const& seqJ, std::string& outStr, EdlibAlignResult& cigar, uint32_t const preI, uint32_t const postI, uint32_t const preJ, uint32_t const postJ) {
91+
buildSuperstring(std::string const& seqI, std::string const& seqJ, std::string& outStr, EdlibAlignResult const& cigar, uint32_t const preI, uint32_t const postI, uint32_t const preJ, uint32_t const postJ) {
9292
int32_t iIdx = 0;
9393
int32_t jIdx = 0;
9494
// prefix
@@ -135,7 +135,7 @@ namespace torali
135135

136136
template<typename TAlign>
137137
inline void
138-
convertAlignment(std::string const& query, TAlign& align, EdlibAlignMode const modeCode, EdlibAlignResult& cigar, uint32_t const preI, uint32_t const postI, uint32_t const preJ, uint32_t const postJ) {
138+
convertAlignment(std::string const& query, TAlign& align, EdlibAlignMode const modeCode, EdlibAlignResult const& cigar, uint32_t const preI, uint32_t const postI, uint32_t const preJ, uint32_t const postJ) {
139139
// Input alignment
140140
TAlign alignIn;
141141
alignIn.resize(boost::extents[align.shape()[0]][align.shape()[1]]);
@@ -811,7 +811,7 @@ namespace torali
811811
// Get sequence
812812
std::string sequence;
813813
sequence.resize(rec->core.l_qseq);
814-
uint8_t* seqptr = bam_get_seq(rec);
814+
const uint8_t* seqptr = bam_get_seq(rec);
815815
for (int i = 0; i < rec->core.l_qseq; ++i) sequence[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
816816
int32_t readlen = sequence.size();
817817

@@ -899,9 +899,9 @@ namespace torali
899899
computeMSA = true;
900900
// Lazy loading of references
901901
if (sndSeq == NULL) {
902-
int32_t seqlen = -1;
903-
std::string tname(hdr->target_name[refIndex2]);
904-
sndSeq = faidx_fetch_seq(fai, tname.c_str(), 0, hdr->target_len[refIndex2], &seqlen);
902+
int32_t seqlen2 = -1;
903+
std::string tname2(hdr->target_name[refIndex2]);
904+
sndSeq = faidx_fetch_seq(fai, tname2.c_str(), 0, hdr->target_len[refIndex2], &seqlen2);
905905
}
906906
}
907907
} else {

‎src/coverage.h

+5-5
Original file line numberDiff line numberDiff line change
@@ -386,7 +386,7 @@ namespace torali {
386386
// Count aligned basepair (small InDels)
387387
{
388388
uint32_t rp = 0; // reference pointer
389-
uint32_t* cigar = bam_get_cigar(rec);
389+
const uint32_t* cigar = bam_get_cigar(rec);
390390
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {
391391
if (bam_cigar_op(cigar[i]) == BAM_CMATCH) {
392392
for(std::size_t k = 0; k<bam_cigar_oplen(cigar[i]);++k) {
@@ -405,7 +405,7 @@ namespace torali {
405405
bool hasSoftClip = false;
406406
bool hasClip = false;
407407
int32_t leadingSC = 0;
408-
uint32_t* cigar = bam_get_cigar(rec);
408+
const uint32_t* cigar = bam_get_cigar(rec);
409409
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {
410410
if (bam_cigar_op(cigar[i]) == BAM_CSOFT_CLIP) {
411411
hasClip = true;
@@ -437,7 +437,7 @@ namespace torali {
437437
// Get sequence
438438
std::string sequence;
439439
sequence.resize(rec->core.l_qseq);
440-
uint8_t* seqptr = bam_get_seq(rec);
440+
const uint8_t* seqptr = bam_get_seq(rec);
441441
for (int i = 0; i < rec->core.l_qseq; ++i) sequence[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
442442
_adjustOrientation(sequence, itBp->bpPoint, itBp->svt);
443443

@@ -474,7 +474,7 @@ namespace torali {
474474
if (++refAlignedReadCount[file_c][itBp->id] % 2) {
475475
TQuality quality;
476476
quality.resize(rec->core.l_qseq);
477-
uint8_t* qualptr = bam_get_qual(rec);
477+
const uint8_t* qualptr = bam_get_qual(rec);
478478
for (int i = 0; i < rec->core.l_qseq; ++i) quality[i] = qualptr[i];
479479
uint32_t rq = _getAlignmentQual(alignRef, quality);
480480
if (rq >= c.minGenoQual) {
@@ -487,7 +487,7 @@ namespace torali {
487487
} else {
488488
TQuality quality;
489489
quality.resize(rec->core.l_qseq);
490-
uint8_t* qualptr = bam_get_qual(rec);
490+
const uint8_t* qualptr = bam_get_qual(rec);
491491
for (int i = 0; i < rec->core.l_qseq; ++i) quality[i] = qualptr[i];
492492
uint32_t aq = _getAlignmentQual(alignAlt, quality);
493493
if (aq >= c.minGenoQual) {

‎src/gaf.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -33,8 +33,8 @@ namespace torali
3333
std::vector<int8_t> cigarop;
3434
std::vector<uint32_t> cigarlen;
3535

36-
AlignRecord() : qstart(0), hap('*'), seed(0) {}
37-
AlignRecord(int32_t const q, std::size_t const s) : qstart(q), hap('*'), seed(s) {}
36+
AlignRecord() : qlen(0), qstart(0), qend(0), plen(0), pstart(0), pend(0), matches(0), alignlen(0), mapq(0), strand('*'), hap('*'), seed(0) {}
37+
AlignRecord(int32_t const q, std::size_t const s) : qlen(0), qstart(q), qend(0), plen(0), pstart(0), pend(0), matches(0), alignlen(0), mapq(0), strand('*'), hap('*'), seed(s) {}
3838

3939
bool operator<(const AlignRecord& s2) const {
4040
return ((seed < s2.seed) || ((seed == s2.seed) && (qstart < s2.qstart)));

‎src/gcbias.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,7 @@ namespace torali
7272
// Sequence
7373
std::string sequence;
7474
sequence.resize(rec->core.l_qseq);
75-
uint8_t* seqptr = bam_get_seq(rec);
75+
const uint8_t* seqptr = bam_get_seq(rec);
7676
for (int i = 0; i < rec->core.l_qseq; ++i) sequence[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
7777

7878
// Reference slice
@@ -81,7 +81,7 @@ namespace torali
8181
// Percent identity
8282
uint32_t rp = 0; // reference pointer
8383
uint32_t sp = 0; // sequence pointer
84-
uint32_t* cigar = bam_get_cigar(rec);
84+
const uint32_t* cigar = bam_get_cigar(rec);
8585
int32_t matchCount = 0;
8686
int32_t mismatchCount = 0;
8787
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {

‎src/genotype.h

+7-8
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@ namespace torali
3030
inline int32_t
3131
_readStart(bam1_t* rec) {
3232
uint32_t rp = rec->core.pos;
33-
uint32_t* cigar = bam_get_cigar(rec);
33+
const uint32_t* cigar = bam_get_cigar(rec);
3434
if (rec->core.n_cigar) {
3535
if ((bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) || (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP)) {
3636
if (rp > bam_cigar_oplen(cigar[0])) rp -= bam_cigar_oplen(cigar[0]);
@@ -43,7 +43,7 @@ namespace torali
4343
inline int32_t
4444
_readEnd(bam1_t* rec) {
4545
uint32_t rp = rec->core.pos;
46-
uint32_t* cigar = bam_get_cigar(rec);
46+
const uint32_t* cigar = bam_get_cigar(rec);
4747
if (rec->core.n_cigar) {
4848
for (uint32_t i = 0; i < rec->core.n_cigar; ++i) {
4949
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF) || (bam_cigar_op(cigar[i]) == BAM_CDEL) || (bam_cigar_op(cigar[i]) == BAM_CREF_SKIP)) rp += bam_cigar_oplen(cigar[i]);
@@ -61,7 +61,7 @@ namespace torali
6161
uint32_t sp = 0; // sequence pointer
6262

6363
// Parse the CIGAR
64-
uint32_t* cigar = bam_get_cigar(rec);
64+
const uint32_t* cigar = bam_get_cigar(rec);
6565
if (rec->core.n_cigar) {
6666
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {
6767
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF)) {
@@ -93,7 +93,6 @@ namespace torali
9393
inline void
9494
genotypeLR(TConfig& c, std::vector<StructuralVariantRecord>& svs, TJunctionMap& jctMap, TReadCountMap& covMap) {
9595
typedef std::vector<StructuralVariantRecord> TSVs;
96-
typedef std::vector<uint8_t> TQuality;
9796
if (svs.empty()) return;
9897

9998
// Open file handles
@@ -136,7 +135,7 @@ namespace torali
136135
boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
137136
std::cerr << '[' << boost::posix_time::to_simple_string(now) << "] " << "SV annotation" << std::endl;
138137

139-
faidx_t* fai = fai_load(c.genome.string().c_str());
138+
const faidx_t* fai = fai_load(c.genome.string().c_str());
140139
for(int32_t refIndex=0; refIndex < (int32_t) hdr[0]->n_targets; ++refIndex) {
141140
// Fetch breakpoints
142141
typedef std::multimap<int32_t, int32_t> TBreakpointMap;
@@ -177,7 +176,7 @@ namespace torali
177176
// Annotate coverage
178177
{
179178
uint32_t rp = rec->core.pos; // reference pointer
180-
uint32_t* cigar = bam_get_cigar(rec);
179+
const uint32_t* cigar = bam_get_cigar(rec);
181180
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {
182181
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF)) {
183182
for(uint32_t k = 0; k < bam_cigar_oplen(cigar[i]); ++k, ++rp) {
@@ -244,8 +243,8 @@ namespace torali
244243
// Load sequence
245244
if (sequence.empty()) {
246245
sequence.resize(rec->core.l_qseq);
247-
uint8_t* seqptr = bam_get_seq(rec);
248-
for (int i = 0; i < rec->core.l_qseq; ++i) sequence[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
246+
const uint8_t* seqptr = bam_get_seq(rec);
247+
for (int ik = 0; ik < rec->core.l_qseq; ++ik) sequence[ik] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, ik)];
249248
}
250249
//std::cerr << hdr[file_c]->target_name[refIndex] << ":" << svs[svid].svStart << "-" << svs[svid].svEnd << "," << svs[svid].svt << "," << (int) (rec->core.flag & BAM_FREVERSE) << "," << ((pos == svs[svid].svStart) ? "Start" : "End") << std::endl;
251250
std::string ref = boost::to_upper_copy(std::string(seq + pos - offset, seq + pos + offset));

‎src/gfa.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -38,8 +38,8 @@ namespace torali
3838
uint32_t mapq;
3939

4040
LinkCargo() {}
41-
LinkCargo(Link const lk) : fromfwd(lk.fromfwd), tofwd(lk.tofwd), from(lk.from), to(lk.to), support(0), mapq(0) {}
42-
LinkCargo(bool const fv, bool const tv, uint32_t const fr, uint32_t tos) : fromfwd(fv), tofwd(tv), from(fr), to(tos), support(0) {}
41+
explicit LinkCargo(Link const lk) : fromfwd(lk.fromfwd), tofwd(lk.tofwd), from(lk.from), to(lk.to), support(0), mapq(0) {}
42+
LinkCargo(bool const fv, bool const tv, uint32_t const fr, uint32_t tos) : fromfwd(fv), tofwd(tv), from(fr), to(tos), support(0), mapq(0) {}
4343

4444
bool operator<(const LinkCargo& l2) const {
4545
return ((from < l2.from) || ((from==l2.from) && (to < l2.to)));

‎src/junction.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -350,7 +350,7 @@ namespace torali
350350
uint32_t sp = 0; // sequence pointer
351351

352352
// Parse the CIGAR
353-
uint32_t* cigar = bam_get_cigar(rec);
353+
const uint32_t* cigar = bam_get_cigar(rec);
354354
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {
355355
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF)) {
356356
sp += bam_cigar_oplen(cigar[i]);
@@ -546,8 +546,8 @@ namespace torali
546546
for(uint32_t svt = 0; svt < altSR.size(); ++svt) {
547547
//std::cerr << '[' << boost::posix_time::to_simple_string(boost::posix_time::second_clock::local_time()) << "] " << "SVT Size: " << svt << ',' << altSR[svt].size() << std::endl;
548548
if (altSR[svt].empty()) continue;
549-
for(uint32_t i = 0; i < altSR[svt].size(); ++i) {
550-
if (validSR.find(altSR[svt][i].id) != validSR.end()) newValidSR.insert(altSR[svt][i].id);
549+
for(uint32_t ik = 0; ik < altSR[svt].size(); ++ik) {
550+
if (validSR.find(altSR[svt][ik].id) != validSR.end()) newValidSR.insert(altSR[svt][ik].id);
551551
}
552552
}
553553
validSR = newValidSR;

‎src/merge.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -502,7 +502,7 @@ void _outputSelectedIntervals(MergeConfig& c, TGenomeIntervals const& iSelected,
502502
bcf_update_info_int32(hdr_out, rout, "CIPOS", cipos, 2);
503503
bcf_update_info_int32(hdr_out, rout, "CIEND", ciend, 2);
504504
if (precise) {
505-
int32_t tmpi = srMapQuality;
505+
tmpi = srMapQuality;
506506
bcf_update_info_int32(hdr_out, rout, "SRMAPQ", &tmpi, 1);
507507
bcf_update_info_int32(hdr_out, rout, "INSLEN", &inslenVal, 1);
508508
bcf_update_info_int32(hdr_out, rout, "HOMLEN", &homlenVal, 1);
@@ -1064,8 +1064,8 @@ int merge(int argc, char **argv) {
10641064
uint32_t chunks = ((c.files.size() - 1) / c.chunksize) + 1;
10651065
std::vector<boost::filesystem::path> chunkCollect(chunks);
10661066
for(uint32_t ic = 0; ic < chunks; ++ic) {
1067-
boost::uuids::uuid uuid = boost::uuids::random_generator()();
1068-
std::string chunkfile = "chunk" + boost::lexical_cast<std::string>(ic) + "_" + boost::lexical_cast<std::string>(uuid) + ".bcf";
1067+
boost::uuids::uuid uuid2 = boost::uuids::random_generator()();
1068+
std::string chunkfile = "chunk" + boost::lexical_cast<std::string>(ic) + "_" + boost::lexical_cast<std::string>(uuid2) + ".bcf";
10691069
chunkCollect[ic] = chunkfile;
10701070
c.files.clear();
10711071
for(uint32_t k = ic * c.chunksize; ((k < ((ic+1) * c.chunksize)) && (k < fileRestore.size())); ++k) c.files.push_back(fileRestore[k]);

‎src/shortpe.h

+2-2
Original file line numberDiff line numberDiff line change
@@ -117,7 +117,7 @@ namespace torali
117117
if (svid == (int32_t) svs[svid].id) { // Should be always true
118118
std::string sequence;
119119
sequence.resize(rec->core.l_qseq);
120-
uint8_t* seqptr = bam_get_seq(rec);
120+
const uint8_t* seqptr = bam_get_seq(rec);
121121
for (int i = 0; i < rec->core.l_qseq; ++i) sequence[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
122122

123123
// Adjust orientation
@@ -318,7 +318,7 @@ namespace torali
318318
uint32_t sp = 0; // sequence pointer
319319

320320
// Parse the CIGAR
321-
uint32_t* cigar = bam_get_cigar(rec);
321+
const uint32_t* cigar = bam_get_cigar(rec);
322322
for (std::size_t i = 0; i < rec->core.n_cigar; ++i) {
323323
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF)) {
324324
sp += bam_cigar_oplen(cigar[i]);

‎src/split.h

+4-4
Original file line numberDiff line numberDiff line change
@@ -80,7 +80,7 @@ namespace torali
8080

8181
// Check for single soft-clip
8282
unsigned int numSoftClip = 0;
83-
uint32_t* cigar = bam_get_cigar(rec);
83+
const uint32_t* cigar = bam_get_cigar(rec);
8484
for (unsigned int i = 0; i < rec->core.n_cigar; ++i) {
8585
if (bam_cigar_op(cigar[i]) == BAM_CSOFT_CLIP) {
8686
++numSoftClip;
@@ -96,7 +96,7 @@ namespace torali
9696
typedef std::vector<uint8_t> TQuality;
9797
TQuality quality;
9898
quality.resize(rec->core.l_qseq);
99-
uint8_t* qualptr = bam_get_qual(rec);
99+
const uint8_t* qualptr = bam_get_qual(rec);
100100
for (int i = 0; i < rec->core.l_qseq; ++i) quality[i] = qualptr[i];
101101

102102
// Get soft-clips
@@ -114,7 +114,7 @@ namespace torali
114114
else leadingSC = false;
115115
splitPoint = rec->core.pos + alen;
116116
unsigned int qualSum = 0;
117-
for(unsigned int i = alen; i < (alen+clipSize); ++i) qualSum += quality[i];
117+
for(unsigned int ik = alen; ik < (alen+clipSize); ++ik) qualSum += quality[ik];
118118
meanQuality = qualSum / clipSize;
119119
}
120120
}
@@ -462,7 +462,7 @@ namespace torali
462462

463463

464464
inline void
465-
editDistanceVec(std::string const& seqI, std::string const& seqJ, EdlibAlignResult& cigar, std::vector<uint32_t>& dist) {
465+
editDistanceVec(std::string const& seqI, std::string const& seqJ, EdlibAlignResult const& cigar, std::vector<uint32_t>& dist) {
466466
// Fill edit distance vector
467467
dist.resize(seqI.size());
468468
std::fill(dist.begin(), dist.end(), 0);

‎src/tags.h

+1-1
Original file line numberDiff line numberDiff line change
@@ -137,7 +137,7 @@ namespace torali {
137137
// Initialize breakpoint
138138
template<typename TBreakpoint>
139139
inline void
140-
_initBreakpoint(bam_hdr_t* hdr, TBreakpoint& bp, int32_t const boundary, int32_t const svt) {
140+
_initBreakpoint(bam_hdr_t const* hdr, TBreakpoint& bp, int32_t const boundary, int32_t const svt) {
141141
if (_translocation(svt)) {
142142
bp.svStartBeg = std::max(0, bp.svStart - boundary);
143143
bp.svStartEnd = std::min((int32_t) (hdr->target_len[bp.chr]), bp.svStart + boundary);

‎src/util.h

+6-9
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@ namespace torali
7373

7474

7575
inline uint32_t
76-
infixStart(EdlibAlignResult& cigar) {
76+
infixStart(EdlibAlignResult const& cigar) {
7777
int32_t tIdx = cigar.endLocations[0];
7878
for (int32_t i = 0; i < cigar.alignmentLength; i++) {
7979
if (cigar.alignment[i] != EDLIB_EDOP_INSERT) tIdx--;
@@ -83,12 +83,12 @@ namespace torali
8383
}
8484

8585
inline uint32_t
86-
infixEnd(EdlibAlignResult& cigar) {
86+
infixEnd(EdlibAlignResult const& cigar) {
8787
return cigar.endLocations[0];
8888
}
8989

9090
inline void
91-
printAlignmentPretty(std::string const& query, std::string const& target, EdlibAlignMode const modeCode, EdlibAlignResult& align) {
91+
printAlignmentPretty(std::string const& query, std::string const& target, EdlibAlignMode const modeCode, EdlibAlignResult const& align) {
9292
int32_t tIdx = -1;
9393
int32_t qIdx = -1;
9494
if (modeCode == EDLIB_MODE_HW) {
@@ -130,7 +130,7 @@ namespace torali
130130
}
131131

132132
inline void
133-
printAlignment(std::string const& seqI, std::string const& seqJ, EdlibAlignMode const modeCode, EdlibAlignResult& cigar) {
133+
printAlignment(std::string const& seqI, std::string const& seqJ, EdlibAlignMode const modeCode, EdlibAlignResult const& cigar) {
134134
int32_t tIdx = -1;
135135
int32_t qIdx = -1;
136136
uint32_t missingEnd = 0;
@@ -142,9 +142,6 @@ namespace torali
142142
if (cigar.alignment[i] != EDLIB_EDOP_INSERT) tIdx--;
143143
}
144144
if (tIdx >= 0) missingStart = tIdx + 1;
145-
}
146-
// infix alignment, fix start
147-
if ((modeCode == EDLIB_MODE_HW) || (modeCode == EDLIB_MODE_SHW)) {
148145
if (missingStart) {
149146
for (uint32_t j = 0; j < missingStart; ++j) std::cerr << '-';
150147
}
@@ -428,7 +425,7 @@ namespace torali
428425
}
429426

430427
inline uint32_t sequenceLength(bam1_t const* rec) {
431-
uint32_t* cigar = bam_get_cigar(rec);
428+
const uint32_t* cigar = bam_get_cigar(rec);
432429
uint32_t slen = 0;
433430
for (uint32_t i = 0; i < rec->core.n_cigar; ++i)
434431
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF) || (bam_cigar_op(cigar[i]) == BAM_CINS) || (bam_cigar_op(cigar[i]) == BAM_CSOFT_CLIP) || (bam_cigar_op(cigar[i]) == BAM_CHARD_CLIP)) slen += bam_cigar_oplen(cigar[i]);
@@ -442,7 +439,7 @@ namespace torali
442439
}
443440

444441
inline uint32_t alignmentLength(bam1_t const* rec) {
445-
uint32_t* cigar = bam_get_cigar(rec);
442+
const uint32_t* cigar = bam_get_cigar(rec);
446443
uint32_t alen = 0;
447444
for (uint32_t i = 0; i < rec->core.n_cigar; ++i)
448445
if ((bam_cigar_op(cigar[i]) == BAM_CMATCH) || (bam_cigar_op(cigar[i]) == BAM_CEQUAL) || (bam_cigar_op(cigar[i]) == BAM_CDIFF) || (bam_cigar_op(cigar[i]) == BAM_CDEL) || (bam_cigar_op(cigar[i]) == BAM_CREF_SKIP)) alen += bam_cigar_oplen(cigar[i]);

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