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Fix warnings #4

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Fix warnings #4

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40bb785
param.cpp: Remove \r at end of line
donald Oct 7, 2017
35c2204
param.c: Remove dangling whitespace
donald Oct 7, 2017
59a9872
param.cpp: Avoid narrowing conversation warnings
donald Oct 7, 2017
a7bd5a7
Fix more warnings
donald Oct 7, 2017
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8 changes: 4 additions & 4 deletions align.cpp
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Expand Up @@ -166,8 +166,8 @@ void SingleAlign::ConvertBinaySeq() {


void SingleAlign::SnpAlign(RefSeq &ref, bit32_t mode) {
bit32_t i,j,jj1,jj,m, modeindex, cmodeindex, mc, h, read_chain_index_mask, *_refloc0;
Hit prefetch_hit, _hHit;
bit32_t i,j,jj,m, modeindex, cmodeindex, mc, h, read_chain_index_mask, *_refloc0;
Hit _hHit;

//cout<<_pread->seq<<endl;
if(param.RRBS_flag){ //RRBS mode
Expand Down Expand Up @@ -370,7 +370,7 @@ void SingleAlign::SortHits4PE(int n) {
}

int SingleAlign::TrimAdapter() {
bit32_t i,j,k,m,m0, pos;
bit32_t i,k,m0, pos;
raw_readlen=_pread->seq.size();
for(i=0; i<param.n_adapter; i++){
for(pos=param.seed_size+param.index_interval-1;pos<_pread->seq.size()-4;pos++){
Expand Down Expand Up @@ -416,7 +416,7 @@ int SingleAlign::RunAlign(RefSeq &ref) {
}

void SingleAlign::ReorderSeed(RefSeq &ref) {
bit32_t i,ii,s, total, tt;
bit32_t i,ii, total, tt;
//for(i=0;i<map_readlen-param.seed_size;i++) {disp_bfa(param.map3to4(seed_array[i])); cout<<i<<":"<<ref.index2[seed_array[i]].n[0]<<":"<<ref.index2[seed_array[i]].n[1]<<endl;}
for(read_chain_index=0;read_chain_index<2;read_chain_index++) {
if(!xflag_chain[read_chain_index]) continue;
Expand Down
8 changes: 4 additions & 4 deletions align.h
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Expand Up @@ -118,9 +118,9 @@ inline void SingleAlign::CountMismatch(bit64_t *q, bit32_t offset, bit64_t *s) {
}
}
else {
if((tmp_snp=N_count+param.XM64((((*q)>>offset)&param.XC64(*s)^(*s))&((q[FIXELEMENT])>>offset)))>snp_thres) return;
if((tmp_snp=N_count+param.XM64(((((*q)>>offset)&param.XC64(*s))^(*s))&((q[FIXELEMENT])>>offset)))>snp_thres) return;
for(bit32_t i=1;i<FIXELEMENT;i++) {
if((tmp_snp+=param.XM64(((((q[i-1]<<1)<<(63-offset))|q[i]>>offset)&param.XC64(s[i])^s[i])&(((q[FIXELEMENT-1+i]<<1)<<(63-offset))|q[i+FIXELEMENT]>>offset)))>snp_thres) return;
if((tmp_snp+=param.XM64((((((q[i-1]<<1)<<(63-offset))|q[i]>>offset)&param.XC64(s[i]))^s[i])&(((q[FIXELEMENT-1+i]<<1)<<(63-offset))|q[i+FIXELEMENT]>>offset)))>snp_thres) return;
}
/*
tmp_snp=N_count;
Expand All @@ -134,7 +134,7 @@ inline void SingleAlign::CountMismatch(bit64_t *q, bit32_t offset, bit64_t *s) {

inline bit32_t SingleAlign::MismatchPattern0(bit64_t *q, bit64_t *s, bit32_t offset) {
register bit64_t tmp;
bit32_t *mm_array; int i, j,jj, ss=0;
bit32_t *mm_array,i;int j,jj, ss=0;
//cout<<"in MMpattern() gap_index:"<<gap_index<<endl;
//cout<<" offset="<<seglen_offset<<" end_element="<<end_element<<" end_offset="<<end_offset<<endl;
mm_array=mm_index[0];
Expand Down Expand Up @@ -171,7 +171,7 @@ inline bit32_t SingleAlign::MismatchPattern0(bit64_t *q, bit64_t *s, bit32_t off

inline bit32_t SingleAlign::MismatchPattern1(bit64_t *q, bit64_t *s, bit32_t gap_index, bit32_t offset) {
register bit64_t tmp; register bit32_t shift;
bit32_t *mm_array; int i,ii, j,jj, ss=0;
bit32_t *mm_array,i; int ii, j,jj, ss=0;
//cout<<"in MMpattern() gap_index:"<<gap_index<<endl;
//cout<<"shift="<<(1-((int)gap_index%2)*2)*((int)gap_index+1)/2<<" offset="<<seglen_offset<<" end_element="<<end_element;
//cout<<" end_offset="<<end_offset<<endl;
Expand Down
5 changes: 2 additions & 3 deletions dbseq.cpp
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Expand Up @@ -138,7 +138,7 @@ void RefSeq::UnmaskRegion() {
}

void RefSeq::find_CCGG() {
bit32_t tmp_offset,tmp_max, seedloc, right=0xffffffffu, seglen; int i,j;
bit32_t tmp_offset,tmp_max, seedloc, right=0xffffffffu, seglen,i,j;
vector<ref_loc_t> tmpset_index_BSW[50], tmpset_index_BSC[50];
vector<pair<ref_loc_t, bit32_t> > tmp_CCGG_sites;
//vector<pair<ref_loc_t, bit32_t> >::iterator rit;
Expand Down Expand Up @@ -378,7 +378,7 @@ void RefSeq::AllocIndex() {

void RefSeq::ReleaseIndex() {
bit32_t i;
KmerLoc *v; KmerLoc2 *u;
KmerLoc *v;
if(param.RRBS_flag){
for(i=0,v=index; i<total_kmers; i++,v++) {
if(v->n1) delete [] v->loc1;
Expand Down Expand Up @@ -461,7 +461,6 @@ void RefSeq::t_FillIndex(bit32_t ref_chain) {
}

void RefSeq::CreateIndex() {
bit32_t i;
InitialIndex();
CalKmerFreq();
AllocIndex();
Expand Down
4 changes: 2 additions & 2 deletions gzstream/Makefile
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Expand Up @@ -78,10 +78,10 @@ test_gunzip : test_gunzip.o libgzstream.a
${CXX} -o test_gunzip test_gunzip.o ${LDFLAGS}

clean :
rm *.o libgzstream.a
rm -f *.o libgzstream.a

cleanall :
rm *.o libgzstream.a test_gzip test_gunzip
rm -f *.o libgzstream.a test_gzip test_gunzip

# ============================================================================
# EOF
Expand Down
13 changes: 8 additions & 5 deletions main.cpp
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Expand Up @@ -409,15 +409,16 @@ void RunProcess(void) {
else message<<"\tmax number of mismatches: read_length * "<<param.max_snp_num-100<<"% ";
message<<" \tmax gap size: "<<param.gap<<" \tkmer cut-off ratio: "<<param.max_kmer_ratio<<" \tmax multi-hits: "<<param.max_num_hits<<endl;
message<<"\tquality cutoff: "<<(int)param.qual_threshold<<" \tbase quality char: '"<<param.zero_qual<<"'"<<" \tmax Ns: "<<param.max_ns;
if(param.max_readlen<(FIXELEMENT-1)*SEGLEN) message<<" \thard clip length: "<<param.max_readlen; message<<endl;
if(param.max_readlen<(FIXELEMENT-1)*SEGLEN) message<<" \thard clip length: "<<param.max_readlen<<endl;
if(param.pairend||param.RRBS_flag) message<<"\tmin fragment size: "<<param.min_insert<<" \tmax fragemt size: "<<param.max_insert<<endl;
if(param.nt3) message<<"\t3-nucleotide alignment mode: "<<param.read_nt<<" <=> "<<param.ref_nt;
else message<<"\twildcard alignment mode: "<<param.read_nt<<" in reads => "<<param.ref_nt<<" in reference";
message<<" \tseed size: "<<param.seed_size<<" \tindex interval: "<<param.index_interval<<endl;
message<<"\talignment report: ";
if(param.report_repeat_hits==0) message<<"unique alignments only";
if(param.report_repeat_hits==1) message<<"unique + one random multiple alignments";
if(param.report_repeat_hits==2) message<<"unique + all multiple alignments"; message<<endl;
if(param.report_repeat_hits==2) message<<"unique + all multiple alignments";
message<<endl;
if(param.pairend){
message<<"\tmapping strand (read_1): ++,-+";
if(param.chains) message<< ",+-,--";
Expand All @@ -434,15 +435,16 @@ void RunProcess(void) {
message<<"\tRRBS digestion site: ";
for(bit32_t i=0; i<param.digest_site.size(); i++)
message<<param.digest_site[i].substr(0,param.digest_pos[i])<<'-'<<param.digest_site[i].substr(param.digest_pos[i])<<" ";
message<<endl;
message<<endl;
}
info(2);
string err_msg;
//pair-end alignment
if(param.pairend) {
message<<"[bsmap] @"<<Curr_Time()<<" \tPair-end alignment("<<param.num_procs<<" threads),"; info(1);
message<<" \tstart from read pair #"<<param.read_start;
if(~param.read_end) message<<" \tend at read pair #"<<param.read_end; info(2); message<<endl; info(1);
if(~param.read_end) message<<" \tend at read pair #"<<param.read_end;
info(2); message<<endl; info(1);
err_msg="failed to open read file #1 (check -a option): ";
message<<"\tInput read file #1: "<<query_a_file;
param.gz_input=check_ifile(query_a_file, err_msg);
Expand Down Expand Up @@ -524,7 +526,8 @@ void RunProcess(void) {
else {
message<<"[bsmap] @"<<Curr_Time()<<" \tSingle-end alignment("<<param.num_procs<<" threads),"; info(1);
message<<" \tstart from read #"<<param.read_start;
if(~param.read_end) message<<" \tend at read #"<<param.read_end; info(2); cerr<<endl; info(1);
if(~param.read_end) message<<" \tend at read #"<<param.read_end;
info(2); cerr<<endl; info(1);
err_msg="failed to open read file (check -a option): ";
message<<"\tInput read file: "<<query_a_file;
param.gz_input=check_ifile(query_a_file, err_msg);
Expand Down
3 changes: 1 addition & 2 deletions pairs.cpp
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Expand Up @@ -131,7 +131,7 @@ int PairAlign::GetPairs(bit32_t na, bit32_t nb)

int PairAlign::RunAlign(RefSeq &ref)
{
bit32_t n,i,j,seedseg_num;
bit32_t n,i,j;

for(i=0; i<=MAXSNPS*2; i++) _cur_n_hits[i]=0;
for(i=0; i<=MAXSNPS; i++) for(j=0; j<=MAXSNPS; j++) checked_pair_mismatch[i][j]=0;
Expand All @@ -142,7 +142,6 @@ int PairAlign::RunAlign(RefSeq &ref)
_sa.seedseg_num=min((bit32_t)((_sa._pread->seq.size()-param.index_interval+1)/param.seed_size),_sa.read_max_snp_num+1);
_sb.seedseg_num=min((bit32_t)((_sb._pread->seq.size()-param.index_interval+1)/param.seed_size),_sb.read_max_snp_num+1);

seedseg_num=max(_sa.seedseg_num,_sb.seedseg_num);
_sa.ConvertBinaySeq();
_sb.ConvertBinaySeq();
_sa.snp_thres=_sa.read_max_snp_num;
Expand Down