[med-svn] [Git][med-team/libpsortb][master] 3 commits: Drop unused debug functions
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Apr 11 14:54:44 BST 2024
Andreas Tille pushed to branch master at Debian Med / libpsortb
Commits:
3d18fdf5 by Andreas Tille at 2024-04-11T15:24:54+02:00
Drop unused debug functions
- - - - -
17467cbe by Andreas Tille at 2024-04-11T15:53:01+02:00
Fix implicit declaration
- - - - -
cc41e139 by Andreas Tille at 2024-04-11T15:54:15+02:00
Add DEP3 Forwarded field
- - - - -
6 changed files:
- debian/changelog
- + debian/patches/fix-implicit-declaration.patch
- + debian/patches/remove_unused_debug_functions.patch
- debian/patches/series
- debian/patches/use_debian_packaged_libs.patch
- debian/patches/use_debian_packaged_libsvm.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libpsortb (1.0+dfsg-6) UNRELEASED; urgency=medium
+
+ * Drop unused debug functions
+ * Fix implicit declaration
+ Closes: #1066475
+ * Add DEP3 Forwarded field
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Apr 2024 15:13:23 +0200
+
libpsortb (1.0+dfsg-5) unstable; urgency=medium
* Versioned Build-Depends: d-shlibs (>= 0.84)
=====================================
debian/patches/fix-implicit-declaration.patch
=====================================
@@ -0,0 +1,46 @@
+Description: Fix implicit declaration
+ Please note: Adding two prototypes directly to debug_funcs.c is hackish but
+ some declarations in funcs.h are conflicting with the implementation ind
+ debug_funcs.c thus it can't be simply included without furtherr changes
+Bug-Debian: https://bugs.debian.org/1066475
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 11 Apr 2024 15:13:23 +0200
+Forwarded: No (orphaned upstream)
+
+--- a/modhmm0.92b/debug_funcs.c
++++ b/modhmm0.92b/debug_funcs.c
+@@ -1,11 +1,13 @@
+ #include <stdlib.h>
+ #include <stdio.h>
+
+-
++//there are conflicting definitions remaining.
++//#include "funcs.h"
++int get_mtx_index(int,int,int);
++int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet);
+
+ #include "structs.h"
+
+-
+ void dump_trans_matrix(int nr_rows, int nr_cols, double *mtx)
+ {
+ int i,j;
+--- a/modhmm0.92b/funcs.h
++++ b/modhmm0.92b/funcs.h
+@@ -167,6 +167,7 @@ int read_prior_file(struct emission_diri
+ int read_frequencies(FILE *freqfile, double **aa_freqs);
+ int read_frequencies_multi(FILE *freqfile, double **aa_freqsp, double **aa_freqsp_2, double **aa_freqsp_3, double **aa_freqsp_4);
+ int read_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet);
++int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet);
+ int locked_state(struct hmm_s *hmmp, int v);
+ int locked_state_multi(struct hmm_multi_s *hmmp, int v);
+ int get_best_reliability_score(double reliability_score_1, double reliability_score_2, double reliability_score_3);
+@@ -198,6 +199,8 @@ void get_reverse_seq_multi(struct sequen
+ struct letter_s **reverse_seq_4, struct hmm_multi_s *hmmp, int seq_len);
+
+ /* std calculation funcs */
++void add_to_E_continuous(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
++ int k, int a_size, double *emissions);
+ double get_single_gaussian_statescore(double mu, double sigma_square, double letter);
+ double get_dp_statescore(int a_size, int use_gap_shares, int use_prior_shares, struct msa_letter_s *msa_seq,
+ int p, double *emissions, int vertex, int normalize, double *gap_shares);
=====================================
debian/patches/remove_unused_debug_functions.patch
=====================================
@@ -0,0 +1,671 @@
+Description: Drop unused debug functions
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 11 Apr 2024 15:13:23 +0200
+Forwarded: No (orphaned upstream)
+
+--- a/modhmm0.92b/core_algorithms_multialpha.c
++++ b/modhmm0.92b/core_algorithms_multialpha.c
+@@ -791,8 +791,6 @@ int viterbi_multi(struct hmm_multi_s *hm
+ }
+
+ #ifdef PATH
+- //dump_viterbi_matrix(seq_len + 2, hmmp->nr_v, viterbi_mtxp);
+- //dump_viterbi_path((cur_rowp + w)->prevp);
+ printf("normalized log likelihood for most probable path = %f\n",
+ 0.0 - (((cur_rowp + hmmp->nr_v - 1)->prob) / seq_len));
+ printf("and most probable path is: ");
+--- a/modhmm0.92b/debug_funcs.c
++++ b/modhmm0.92b/debug_funcs.c
+@@ -6,38 +6,6 @@
+ #include "structs.h"
+
+
+-void dump_align_matrix(int nr_rows, int nr_cols, struct align_mtx_element_s *mtx)
+-{
+- int i,j;
+- struct align_mtx_element_s *mtx_tmp;
+- mtx_tmp = mtx;
+-
+- printf("alignment matrix dump:\n");
+- printf("nr rows: %d\n", nr_rows);
+- printf("nr columns: %d\n", nr_cols);
+- printf("scores:\n");
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%d ", mtx_tmp->score);
+- mtx_tmp++;
+- }
+- printf("\n");
+- }
+- printf("\n\n");
+-
+- mtx_tmp = mtx;
+-
+- printf("lasts:\n");
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%c ", mtx->last);
+- mtx++;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+ void dump_trans_matrix(int nr_rows, int nr_cols, double *mtx)
+ {
+ int i,j;
+@@ -54,22 +22,6 @@ void dump_trans_matrix(int nr_rows, int
+ printf("\n");
+ }
+
+-void dump_int_trans_matrix(int nr_rows, int nr_cols, int *mtx)
+-{
+- int i,j;
+- printf("transition matrix dump:\n");
+- printf("nr rows: %d\n", nr_rows);
+- printf("nr columns: %d\n", nr_cols);
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%d ", *mtx);
+- mtx++;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+ void dump_emiss_matrix(int nr_rows, int nr_cols, double *mtx)
+ {
+ int i,j;
+@@ -84,20 +36,6 @@ void dump_emiss_matrix(int nr_rows, int
+ printf("\n");
+ }
+
+-void dump_post_prob_matrix(int nr_rows, int nr_cols, double *mtx)
+-{
+- int i,j;
+- printf("posterior probability matrix dump:\n");
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%f ", *mtx);
+- mtx++;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+ void dump_forward_matrix(int nr_rows, int nr_cols, struct forward_s *mtx)
+ {
+ int i,j;
+@@ -112,37 +50,6 @@ void dump_forward_matrix(int nr_rows, in
+ printf("\n");
+ }
+
+-void dump_viterbi_matrix(int nr_rows, int nr_cols, struct viterbi_s *mtx)
+-{
+- int i,j;
+- struct viterbi_s *mtx_2;
+-
+- mtx_2 = mtx;
+- printf("viterbi matrix dump probs:\n");
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- //printf("%d ", mtx->prev);
+- printf("%f ", mtx->prob);
+- mtx++;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-
+- printf("viterbi matrix dump prevs:\n");
+- for(i = 0; i < nr_rows; i++) {
+- printf("row: %d\n", i);
+- for(j = 0; j < nr_cols; j++) {
+- printf("col: %d = %d \n", j, mtx_2->prev);
+- //printf("%f ", mtx->prob);
+- mtx_2++;
+- }
+- printf("nr_cols = %d\n", j);
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+ void dump_one_best_matrix(int nr_rows, int nr_cols, struct one_best_s *mtx)
+ {
+ int i,j;
+@@ -220,24 +127,6 @@ void dump_from_trans_array(int nr_v, str
+ printf("\n");
+ }
+
+-void dump_subst_mtx(double *mtx, int a_size)
+-{
+- int i,j;
+- int nr_rows = a_size + 1;
+- int nr_cols = a_size;
+- printf("substitution matrix dump:\n");
+- printf("nr rows: %d\n", nr_rows);
+- printf("nr columns: %d\n", nr_cols);
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%f ", *mtx);
+- mtx++;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+ void dump_to_trans_array(int nr_v, struct path_element **array)
+ {
+ int i;
+@@ -354,40 +243,6 @@ void dump_viterbi_label_path(struct vite
+ }
+ }
+
+-void dump_modules(struct hmm_s *hmmp)
+-{
+- int i,j;
+-
+- printf("\nModule dump:\n");
+- for(i = 0 ; i < hmmp->nr_m; i++) {
+- printf("module: %s", (*(hmmp->modules + i))->name);
+- printf("nr_v: %d\n", (*(hmmp->modules + i))->nr_v);
+- printf("vertices: ");
+- for(j = 0; j < (*(hmmp->modules + i))->nr_v;j++) {
+- printf("%d ",*(((*(hmmp->modules + i))->vertices) + j));
+- }
+- printf("\n");
+- }
+-
+-
+-}
+-
+-void dump_multi_modules(struct hmm_multi_s *hmmp)
+-{
+- int i,j;
+-
+- printf("\nModule dump:\n");
+- for(i = 0 ; i < hmmp->nr_m; i++) {
+- printf("module: %s", (*(hmmp->modules + i))->name);
+- printf("nr_v: %d\n", (*(hmmp->modules + i))->nr_v);
+- printf("vertices: ");
+- for(j = 0; j < (*(hmmp->modules + i))->nr_v;j++) {
+- printf("%d ",*(((*(hmmp->modules + i))->vertices) + j));
+- }
+- printf("\n");
+- }
+-}
+-
+ void dump_distrib_groups(int *distrib_groups, int nr_d)
+ {
+ int i,j;
+@@ -468,22 +323,6 @@ void dump_prior_struct(struct emission_d
+ printf("\n");
+ }
+
+-void dump_silent_vertices(struct hmm_s *hmmp)
+-{
+- int i;
+-
+- printf("silent vertices dump: ");
+- for(i = 0;;i++) {
+- if(*(hmmp->silent_vertices + i) == END) {
+- break;
+- }
+- else {
+- printf("%d ", *(hmmp->silent_vertices + i));
+- }
+- }
+- printf("\n");
+-}
+-
+ void dump_silent_vertices_multi(struct hmm_multi_s *hmmp)
+ {
+ int i;
+@@ -500,23 +339,6 @@ void dump_silent_vertices_multi(struct h
+ printf("\n");
+ }
+
+-void dump_locked_vertices(struct hmm_s *hmmp)
+-{
+- int i;
+-
+- printf("locked vertices dump: ");
+- for(i = 0;;i++) {
+- if(*(hmmp->locked_vertices + i) == END) {
+- break;
+- }
+- else {
+- printf("%d ", *(hmmp->locked_vertices + i));
+- }
+- }
+- printf("\n");
+-}
+-
+-
+ void dump_seq(struct letter_s *seq)
+ {
+ int i;
+@@ -533,134 +355,6 @@ void dump_seq(struct letter_s *seq)
+ printf("\n");
+ }
+
+-void dump_seqs(struct sequences_s *seq_infop)
+-{
+- int i,j;
+- struct letter_s *seqsp;
+-
+-
+- printf("seqs dump\n");
+- for(i = 0; i < seq_infop->nr_seqs; i++) {
+- seqsp = (seq_infop->seqs + i)->seq;
+- printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
+- printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
+- while(seqsp->letter[0] != '\0') {
+- j = 0;
+- while(seqsp->letter[j] != '\0') {
+- printf("%c", seqsp->letter[j]);
+- j++;
+- }
+- printf(";");
+- seqsp++;
+- }
+- printf("\n");
+- }
+-}
+-
+-void dump_seqs_multi(struct sequences_multi_s *seq_infop)
+-{
+- int i,j,k;
+- struct letter_s *seqsp;
+-
+- printf("multi alphabet seqs dump\n");
+- printf("nr_seqs = %d\n", seq_infop->nr_seqs);
+- printf("longest_seq = %d\n", seq_infop->longest_seq);
+- printf("shortest_seq = %d\n", seq_infop->shortest_seq);
+- printf("avg_seq_len = %d\n", seq_infop->avg_seq_len);
+- for(i = 0; i < seq_infop->nr_seqs; i++) {
+- for(k = 0; k < seq_infop->nr_alphabets; k++) {
+- if(k == 0) {
+- seqsp = (seq_infop->seqs + i)->seq_1;
+- }
+- if(k == 1) {
+- seqsp = (seq_infop->seqs + i)->seq_2;
+- }
+- if(k == 2) {
+- seqsp = (seq_infop->seqs + i)->seq_3;
+- }
+- if(k == 3) {
+- seqsp = (seq_infop->seqs + i)->seq_4;
+- }
+- printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
+- printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
+- while(seqsp->letter[0] != '\0') {
+- j = 0;
+- while(seqsp->letter[j] != '\0') {
+- printf("%c", seqsp->letter[j]);
+- j++;
+- }
+- printf(";");
+- seqsp++;
+- }
+- printf("\n");
+- }
+- }
+-}
+-
+-void dump_labeled_seqs_multi(struct sequences_multi_s *seq_infop)
+-{
+- int i,j,k;
+- struct letter_s *seqsp;
+-
+- printf("seqs dump\n");
+- for(i = 0; i < seq_infop->nr_seqs; i++) {
+- for(k = 0; k < seq_infop->nr_alphabets; k++) {
+- if(k == 0) {
+- seqsp = (seq_infop->seqs + i)->seq_1;
+- }
+- if(k == 1) {
+- seqsp = (seq_infop->seqs + i)->seq_2;
+- }
+- if(k == 2) {
+- seqsp = (seq_infop->seqs + i)->seq_3;
+- }
+- if(k == 3) {
+- seqsp = (seq_infop->seqs + i)->seq_4;
+- }
+- printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
+- printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
+- while(seqsp->letter[0] != '\0') {
+- j = 0;
+- while(seqsp->letter[j] != '\0') {
+- printf("%c", seqsp->letter[j]);
+- j++;
+- }
+- if(k == 0) {
+- printf("/%c",seqsp->label);
+- }
+- printf(";");
+- seqsp++;
+- }
+- printf("\n");
+- }
+- }
+-}
+-
+-void dump_labeled_seqs(struct sequences_s *seq_infop)
+-{
+- int i,j;
+- struct letter_s *seqsp;
+-
+- printf("seqs dump\n");
+- for(i = 0; i < seq_infop->nr_seqs; i++) {
+- seqsp = (seq_infop->seqs + i)->seq;
+- printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
+- printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
+- while(seqsp->letter[0] != '\0') {
+- j = 0;
+- while(seqsp->letter[j] != '\0') {
+- printf("%c", seqsp->letter[j]);
+- j++;
+- }
+- printf("/%c",seqsp->label);
+- printf(";");
+- seqsp++;
+- }
+- printf("\n");
+- }
+-}
+-
+-
+ void dump_msa_seqs(struct msa_sequences_s *msa_seq_infop, int a_size)
+ {
+ int i,j;
+@@ -842,115 +536,6 @@ void dump_msa_seqs_multi(struct msa_sequ
+ printf("\n\n");
+ }
+
+-
+-void dump_replacement_letters(struct replacement_letter_s *replacement_letters, int a_size)
+-{
+- int i,j;
+- int nr_rows, nr_cols;
+- double *prob_mtx;
+-
+- prob_mtx = replacement_letters->probs;
+- nr_rows = replacement_letters->nr_rl;
+- nr_cols = a_size;
+-
+-
+- printf("replacement letter dump:\n");
+- printf("nr_letters = %d\n", replacement_letters->nr_rl);
+- printf("letters: ");
+- for(i = 0; i < nr_rows;i++) {
+- printf("%c ", (*(replacement_letters->letters + i)));
+- }
+- printf("\nprobs:\n");
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%f ", *prob_mtx);
+- prob_mtx++;;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+-void dump_replacement_letters_multi(struct replacement_letter_multi_s *replacement_letters, int alphabet, int a_size)
+-{
+- int i,j;
+- int nr_rows, nr_cols;
+- double *prob_mtx;
+-
+- if(alphabet == 1) {
+- prob_mtx = replacement_letters->probs_1;
+- nr_rows = replacement_letters->nr_rl_1;
+- }
+- if(alphabet == 2) {
+- prob_mtx = replacement_letters->probs_2;
+- nr_rows = replacement_letters->nr_rl_2;
+- }
+- if(alphabet == 3) {
+- prob_mtx = replacement_letters->probs_3;
+- nr_rows = replacement_letters->nr_rl_3;
+- }
+- if(alphabet == 4) {
+- prob_mtx = replacement_letters->probs_4;
+- nr_rows = replacement_letters->nr_rl_4;
+- }
+- nr_cols = a_size;
+-
+-
+- printf("replacement letter dump:\n");
+- if(alphabet == 1) {
+- printf("nr_letters = %d\n", replacement_letters->nr_rl_1);
+- }
+- if(alphabet == 2) {
+- printf("nr_letters = %d\n", replacement_letters->nr_rl_2);
+- }
+- if(alphabet == 3) {
+- printf("nr_letters = %d\n", replacement_letters->nr_rl_3);
+- }
+- if(alphabet == 4) {
+- printf("nr_letters = %d\n", replacement_letters->nr_rl_4);
+- }
+- printf("letters: ");
+- for(i = 0; i < nr_rows;i++) {
+- if(alphabet == 1) {
+- printf("%c ", (*(replacement_letters->letters_1 + i)));
+- }
+- if(alphabet == 2) {
+- printf("%c ", (*(replacement_letters->letters_2 + i)));
+- }
+- if(alphabet == 3) {
+- printf("%c ", (*(replacement_letters->letters_3 + i)));
+- }
+- if(alphabet == 4) {
+- printf("%c ", (*(replacement_letters->letters_4 + i)));
+- }
+- }
+- printf("\nprobs:\n");
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%f ", *prob_mtx);
+- prob_mtx++;;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+-void dump_calibration_matrix(int nr_rows, int nr_cols, int *mtx)
+-{
+- int i,j;
+- printf("calibration matrix dump:\n");
+- printf("nr rows: %d\n", nr_rows);
+- printf("nr columns: %d\n", nr_cols);
+- for(i = 0; i < nr_rows; i++) {
+- for(j = 0; j < nr_cols; j++) {
+- printf("%d ", *mtx);
+- mtx++;
+- }
+- printf("\n");
+- }
+- printf("\n");
+-}
+-
+ void dump_to_silent_trans_array(int nr_v, int **array)
+ {
+ int i;
+@@ -969,19 +554,6 @@ void dump_to_silent_trans_array(int nr_v
+ printf("\n");
+ }
+
+-void dump_aa_distrib_mtx(struct aa_distrib_mtx_s *aa_distrib_mtxp)
+-{
+- int i;
+-
+- printf("aa_distrib_mtx_dump\n");
+- printf("a_size = %d\n", aa_distrib_mtxp->a_size);
+- for(i = 0; i < aa_distrib_mtxp->a_size;i++) {
+- printf("%f %f %f\n", *(aa_distrib_mtxp->inside_values + i), *(aa_distrib_mtxp->outside_values + i),
+- *(aa_distrib_mtxp->membrane_values + i));
+- }
+-}
+-
+-
+ void dump_v_list(int *sorted_v_list)
+ {
+ int i = 0;
+@@ -1025,17 +597,6 @@ void dump_label_tmp_list(int *list)
+ printf("\n");
+ }
+
+-void dump_labels(char *labels, int nr_labels)
+-{
+- int i;
+-
+- printf("label_dump: \n");
+- for(i = 0; i < nr_labels; i++) {
+- printf("%c ", labels[i]);
+- }
+- printf("\n");
+-}
+-
+ void check_for_corrupt_values(int nr_rows, int nr_cols, double *mtx, char *name)
+ {
+ int v,w;
+@@ -1060,12 +621,3 @@ void check_for_corrupt_values(int nr_row
+ }
+ }
+
+-void dump_weights(double *weights, int nr_seqs)
+-{
+- int i;
+-
+- printf("weight dump:\n");
+- for(i = 0; i < nr_seqs; i++) {
+- printf("%f\n", *(weights + i));
+- }
+-}
+--- a/modhmm0.92b/funcs.h
++++ b/modhmm0.92b/funcs.h
+@@ -264,14 +264,10 @@ void deallocate_row_labelings(struct one
+
+
+ /* debug_funcs */
+-void dump_align_matrix(int nr_rows, int nr_cols, struct align_mtx_element_s *mtx);
+ void dump_trans_matrix(int,int,double*);
+-void dump_int_trans_matrix(int nr_rows, int nr_cols, double *mtx);
+ void dump_emiss_matrix(int,int,double*);
+-void dump_post_prob_matrix(int nr_rows, int nr_cols, double *mtx);
+ void dump_forward_matrix(int,int,struct forward_s*);
+ void dump_backward_matrix(int,int,struct backward_s*);
+-void dump_viterbi_matrix(int nr_rows, int nr_cols, struct viterbi_s *mtx);
+ void dump_one_best_matrix(int, int, struct one_best_s*);
+ void dump_scaling_array(int,double*);
+ void dump_from_trans_array(int,struct path_element**);
+@@ -280,23 +276,14 @@ void dump_viterbi_path(struct viterbi_s*
+ void dump_viterbi_label_path(struct viterbi_s*, struct hmm_s*, struct viterbi_s*, int, int);
+ void dump_T_matrix(int,int,double*);
+ void dump_E_matrix(int,int,double*);
+-void dump_modules(struct hmm_s*);
+ void dump_distrib_groups(int*, int);
+ void dump_trans_tie_groups(struct transition_s*, int);
+ void dump_prior_struct(struct emission_dirichlet_s*);
+-void dump_silent_vertices(struct hmm_s*);
+ void dump_silent_vertices_multi(struct hmm_multi_s *hmmp);
+-void dump_locked_vertices(struct hmm_s*);
+-void dump_seqs(struct sequences_s*);
+-void dump_seqs_multi(struct sequences_multi_s*);
+ void dump_msa_seqs(struct msa_sequences_s*, int);
+ void dump_msa_seqs_multi(struct msa_sequences_s*, struct hmm_multi_s*);
+ void dump_to_silent_trans_array(int, int**);
+-void dump_aa_distrib_mtx(struct aa_distrib_mtx_s *aa_distrib_mtxp);
+ void dump_v_list(int*);
+ void dump_labeling(char*, int);
+ void dump_label_tmp_list(int *list);
+ void check_for_corrupt_values(int nr_rows, int nr_cols, double *mtx, char *name);
+-void dump_subst_mtx(int a_size, double *mtx);
+-void dump_multi_modules(struct hmm_multi_s *hmmp);
+-void dump_weights(double *total_weights, int nr_seqs);
+--- a/modhmm0.92b/std_funcs.c
++++ b/modhmm0.92b/std_funcs.c
+@@ -346,7 +346,6 @@ void get_aa_distrib_mtx(FILE *distribmtx
+ i++;
+ }
+ }
+- //dump_aa_distrib_mtx(aa_distrib_mtxp);
+ }
+
+
+@@ -445,7 +444,6 @@ void get_replacement_letters(FILE *replf
+ }
+ }
+ free(alphabet);
+- //dump_replacement_letters(replacement_lettersp, a_size);
+ }
+
+ void get_replacement_letters_multi(FILE *replfile, struct replacement_letter_multi_s *replacement_lettersp)
+@@ -625,7 +623,6 @@ void get_replacement_letters_multi(FILE
+
+ }
+ free(alphabet);
+- //dump_replacement_letters_multi(replacement_lettersp, l+1, a_size);
+ }
+ }
+
+@@ -980,7 +977,6 @@ int read_subst_matrix(double **mtxpp, FI
+ }
+ }
+ free(alphabet);
+- //dump_subst_mtx(mtxp, a_size);
+ //exit(0);
+ return YES;
+ }
+@@ -1098,7 +1094,6 @@ int read_subst_matrix_multi(double **mtx
+ }
+ }
+ free(alphabet);
+- //dump_subst_mtx(mtxp, a_size);
+ //exit(0);
+ }
+ return YES;
+--- a/modhmm0.92b/readhmm.c
++++ b/modhmm0.92b/readhmm.c
+@@ -169,9 +169,6 @@ int readhmm(FILE *file, struct hmm_multi
+ *(hmmp->locked_vertices + hmmp->nr_v) = END;
+
+ #ifdef DEBUG_RD
+- //dump_locked_vertices(hmmp);
+- //dump_silent_vertices(hmmp);
+- //dump_modules(hmmp);
+ #endif
+
+ /* empty row */
+@@ -445,9 +442,6 @@ int readanhmm(FILE *file, struct hmm_mul
+ *(hmmp->locked_vertices + hmmp->nr_v) = END;
+
+ #ifdef DEBUG_RD
+- //dump_locked_vertices(hmmp);
+- //dump_silent_vertices(hmmp);
+- //dump_modules(hmmp);
+ #endif
+
+ /* empty row */
+--- a/modhmm0.92b/readhmm_multialpha.c
++++ b/modhmm0.92b/readhmm_multialpha.c
+@@ -567,9 +567,6 @@ int readhmm_multialpha(FILE *file, struc
+ *(hmmp->silent_vertices + silent_counter) = END;
+ *(hmmp->locked_vertices + hmmp->nr_v) = END;
+ #ifdef DEBUG_RD
+- //dump_locked_vertices(hmmp);
+- //dump_silent_vertices(hmmp);
+- //dump_multi_modules(hmmp);
+ #endif
+
+ /* empty row */
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
use_debian_packaged_libs.patch
use_debian_packaged_libsvm.patch
+remove_unused_debug_functions.patch
+fix-implicit-declaration.patch
=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -1,6 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 17 Mar 2017 10:23:15 +010
Description: Use Debian packaged libbiosquid and libhmmer2
+Forwarded: Not needed
--- a/Makefile.am
+++ b/Makefile.am
=====================================
debian/patches/use_debian_packaged_libsvm.patch
=====================================
@@ -1,6 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 17 Mar 2017 10:23:15 +010
Description: Use Debian packaged libsvm
+Forwarded: Not needed
--- libpsortb.orig/svmloc/Makefile.am
+++ libpsortb/svmloc/Makefile.am
View it on GitLab: https://salsa.debian.org/med-team/libpsortb/-/compare/e2039b2a53c5fd5ffff4f64a627c7bd88195a537...cc41e1399501b51728f030db578f495ec888368d
--
View it on GitLab: https://salsa.debian.org/med-team/libpsortb/-/compare/e2039b2a53c5fd5ffff4f64a627c7bd88195a537...cc41e1399501b51728f030db578f495ec888368d
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