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Merge branch 'master' of github.com:sim82/papara_nt

Conflicts:
	papara.cpp
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commit c4f821dc16d5403d21f7f174c9638d5b2c424d54 2 parents 41f271e + 5c54775
@sim82 authored
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2  build_papara2.sh
@@ -5,7 +5,7 @@
-g++ -o papara -O3 -march=native -I. -I ivy_mike/src/ -I ublasJama-1.0.2.3 papara.cpp pvec.cpp pars_align_seq.cpp pars_align_gapp_seq.cpp parsimony.cpp sequence_model.cpp papara2_main.cpp blast_partassign.cpp ivy_mike/src/time.cpp ivy_mike/src/tree_parser.cpp ivy_mike/src/getopt.cpp ivy_mike/src/demangle.cpp ivy_mike/src/multiple_alignment.cpp ublasJama-1.0.2.3/EigenvalueDecomposition.cpp -lpthread
+g++ -o papara -O3 -msse4.1 -I. -I ivy_mike/src/ -I ublasJama-1.0.2.3 papara.cpp pvec.cpp pars_align_seq.cpp pars_align_gapp_seq.cpp parsimony.cpp sequence_model.cpp papara2_main.cpp blast_partassign.cpp align_utils.cpp ivy_mike/src/time.cpp ivy_mike/src/tree_parser.cpp ivy_mike/src/getopt.cpp ivy_mike/src/demangle.cpp ivy_mike/src/multiple_alignment.cpp ublasJama-1.0.2.3/EigenvalueDecomposition.cpp -lpthread
#-I/usr/include/boost141/
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4 fasta_random_sample2.cpp
@@ -84,8 +84,8 @@ void process_fasta( std::istream &is, const std::string &primer_name )
ivy_mike::read_fasta( is, names, data, false );
- const size_t n = names.size();
- assert( n == data.size());
+
+ assert( names.size() == data.size());
std::vector<size_t> rind;
for( size_t i = 0; i < names.size(); ++i ) {
2  genassign_blast
@@ -1 +1 @@
-Subproject commit c2c3622dfdfcf886e6759ca6d1856b06cc46c5c3
+Subproject commit 4ede83da89bde865c6e58651fe23bdb196d70ff2
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2  papara.cpp
@@ -496,7 +496,7 @@ const std::vector<int> &references<pvec_t,seq_tag>::ng_map_at( size_t i ) {
//std::vector<int> map;
std::vector< uint8_t > &seq = m_ref_seqs.at(i);
- assert( seq.size() < std::numeric_limits<int>::max() );
+ assert( seq.size() < size_t(std::numeric_limits<int>::max()) );
for( size_t i = 0; i < seq.size(); ++i ) {
bool is_gap = seq_model::pstate_is_gap( seq_model::s2p(seq[i]));
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5 papara.h
@@ -703,10 +703,7 @@ class ref_gap_collector {
// TODO: shouldn't it be possible to infer the state_type from oiter?
template<typename iiter, typename oiter, typename state_type>
void transform( iiter istart, iiter iend, oiter ostart, state_type gap ) const {
-
- size_t s = std::distance(istart, iend);
- assert( s == ref_gaps_.size() - 1 );
-
+ assert( std::distance(istart, iend) == ref_gaps_.size() - 1 );
size_t i = 0;
while( istart != iend ) {
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1  tar_release.sh
@@ -0,0 +1 @@
+tar --exclude 'genassign_blast/*' --exclude 'genassign_blast' --exclude-vcs -c -z -f papara_nt-2.3-alpha.tar.gz papara_nt/
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12 vec_unit.h
@@ -409,6 +409,7 @@ struct vector_unit<int, 4> {
#ifdef __SSE4_1__
return _mm_min_epi32( a, b );
#else
+ #error "probably untested code!"
const vec_t ma = _mm_cmplt_epi32( a, b );
return _mm_or_si128( _mm_and_si128( ma, a ), _mm_andnot_si128( ma, b ) );
#endif
@@ -419,6 +420,7 @@ struct vector_unit<int, 4> {
#ifdef __SSE4_1__
return _mm_max_epi32( a, b );
#else
+ #error "probably untested code!"
const vec_t ma = _mm_cmpgt_epi32( a, b );
return _mm_or_si128( _mm_and_si128( ma, a ), _mm_andnot_si128( ma, b ) );
#endif
@@ -903,9 +905,9 @@ struct vector_unit<double, 4> {
// const static uint64_t SIGN_MASK_U64 = 0x7FFFFFFFFFFFFFFF;
- const static T LARGE_VALUE = 1e8;
- const static T SMALL_VALUE = -1e8;
- const static T BIAS = 0;
+ const static T LARGE_VALUE;// = 1e8;
+ const static T SMALL_VALUE; //= -1e8;
+ const static T BIAS;// = 0;
const static size_t W = 2;
@@ -1027,7 +1029,9 @@ struct vector_unit<double, 4> {
};
-
+const double vector_unit<double,4>::LARGE_VALUE = 1e8;
+const double vector_unit<double,4>::SMALL_VALUE = -1e8;
+const double vector_unit<double,4>::BIAS = 0;
#endif
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