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Update pllmodules to allow for floating point weights #26

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Update pllmodules to allow for floating point weights #26

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83b49af
Update pllmodules to allow for floating point weights
computations Jan 27, 2021
edf8c36
Switches the libpll to the repo branch
computations Jan 28, 2021
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4 changes: 2 additions & 2 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
[submodule "libpll"]
path = libs/libpll
url = https://github.com/xflouris/libpll-2.git
branch = master
url = https://github.com/computations/libpll-2.git
branch = floating_weights
2 changes: 1 addition & 1 deletion libs/libpll
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Submodule libpll updated 11 files
+2 −2 src/core_derivatives.c
+6 −4 src/core_derivatives_avx.c
+5 −3 src/core_derivatives_avx2.c
+10 −10 src/core_likelihood.c
+11 −11 src/core_likelihood_avx.c
+5 −5 src/core_likelihood_avx2.c
+8 −8 src/core_likelihood_sse.c
+2 −2 src/fast_parsimony.c
+3 −3 src/likelihood.c
+6 −6 src/pll.c
+38 −38 src/pll.h
10 changes: 5 additions & 5 deletions src/msa/pll_msa.c
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Expand Up @@ -49,7 +49,7 @@ PLL_EXPORT double * pllmod_msa_empirical_frequencies(pll_partition_t * partition
unsigned int rate_cats = partition->rate_cats;
unsigned int tips = partition->tips;
const pll_state_t * tipmap = partition->tipmap;
const unsigned int * w = partition->pattern_weights;
const double * w = partition->pattern_weights;
double * frequencies;

if ((frequencies = (double *) calloc ((size_t) states, sizeof(double)))
Expand Down Expand Up @@ -146,7 +146,7 @@ PLL_EXPORT double * pllmod_msa_empirical_frequencies(pll_partition_t * partition

void compute_pair_rates(unsigned int states, unsigned int tips,
unsigned long sites, unsigned char ** tipchars,
const unsigned int * w, const pll_state_t * tipmap,
const double * w, const pll_state_t * tipmap,
size_t * state_freq, size_t * pair_rates)
{
unsigned int i, j, k;
Expand Down Expand Up @@ -191,7 +191,7 @@ PLL_EXPORT double * pllmod_msa_empirical_subst_rates(pll_partition_t * partition
unsigned int tips = partition->tips;
unsigned int rate_cats = partition->rate_cats;
const pll_state_t * tipmap = partition->tipmap;
const unsigned int * w = partition->pattern_weights;
const double * w = partition->pattern_weights;
unsigned char ** tipchars = partition->tipchars;

unsigned int n_subst_rates = (states * (states - 1) / 2);
Expand Down Expand Up @@ -287,7 +287,7 @@ PLL_EXPORT double pllmod_msa_empirical_invariant_sites(pll_partition_t *partitio
unsigned int n;
unsigned int n_inv = 0;
unsigned int sites = partition->sites;
const unsigned int * w = partition->pattern_weights;
const double * w = partition->pattern_weights;

/* reset errno */
pll_errno = 0;
Expand Down Expand Up @@ -577,7 +577,7 @@ PLL_EXPORT void pllmod_msa_destroy_errors(pllmod_msa_errors_t * errs)
PLL_EXPORT pllmod_msa_stats_t * pllmod_msa_compute_stats(const pll_msa_t * msa,
unsigned int states,
const pll_state_t * tipmap,
const unsigned int * weights,
const double * weights,
unsigned long stats_mask)
{
if (!msa)
Expand Down
2 changes: 1 addition & 1 deletion src/msa/pll_msa.h
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ PLL_EXPORT void pllmod_msa_destroy_errors(pllmod_msa_errors_t * errs);
PLL_EXPORT pllmod_msa_stats_t * pllmod_msa_compute_stats(const pll_msa_t * msa,
unsigned int states,
const pll_state_t * tipmap,
const unsigned int * weights,
const double * weights,
unsigned long stats_mask);

PLL_EXPORT void pllmod_msa_destroy_stats(pllmod_msa_stats_t * stats);
Expand Down
2 changes: 1 addition & 1 deletion src/tree/pll_tree.c
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Expand Up @@ -989,7 +989,7 @@ pll_utree_t * pllmod_utree_create_parsimony(unsigned int taxon_count,
unsigned int seq_length,
char * const * names,
char * const * sequences,
const unsigned int * site_weights,
const double * site_weights,
const pll_state_t * map,
unsigned int states,
unsigned int attributes,
Expand Down
2 changes: 1 addition & 1 deletion src/tree/pll_tree.h
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Expand Up @@ -390,7 +390,7 @@ pll_utree_t * pllmod_utree_create_parsimony(unsigned int taxon_count,
unsigned int seq_length,
char * const * names,
char * const * sequences,
const unsigned int * site_weights,
const double * site_weights,
const pll_state_t * map,
unsigned int states,
unsigned int attributes,
Expand Down