16 bit integers (#13)

* 8bit->16bit integers

* deleted objects from index, fixed emission table

* added gitignore

* fixed test samples

Co-authored-by: Bogdan Kirilenko <kirilenk@hiller-mac-21.mpi-cbg.de>

.gitignore

@@ -0,0 +1,3 @@
+.idea/
+src/*.o
+cesar

extra/samples/example1.out

@@ -1,4 +1,4 @@
 >referenceExon
                                                                                                     gCCTGGGAACTTCACCTACCACATCCCTGTCAGTAGTGGCACCCCACTGCACCTCAGCCTGACTCTGCAGATGaa                                                                                                    
 >mouse
-ctttcctcatttcctcaggcttcagtatagcatgaggctgaggaggagagagggagaccggcaaagtggccttgcttaggtaccatctttgcccctttaggCTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGaagtgagtgctggtgtgtgggtatgtgtgggggaccatgtggaagccctcagaaaagtgaaagccaagtgcttactaaatttattacgtggagggtccaggc
+ctttcctcatttcctcaggcttcagtatagcatgaggctgaggaggagagagggagaccggcaaagtggccttgcttaggtaccatctttgcccctttagGCTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAAgtgagtgctggtgtgtgggtatgtgtgggggaccatgtggaagccctcagaaaagtgaaagccaagtgcttactaaatttattacgtggagggtccaggc

extra/samples/sample0.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCCAAACCCAAACCCAAACCCAAACCCaa       
 >query
-cttccccatttttatctcatagacCCCAAACCCAAACCCAAACCCAAACCCaagtaaaaa
+cttccccatttttatctcatagACCCCAAACCCAAACCCAAACCCAAACCCAAgtaaaaa

extra/samples/sample1.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCCAAACCCAAACCCAAACCCAAACCCaa       
 >query
-cttccccatttttatctcatag--CCCAAACCCAAACCCAAACCCAAACCCaagtaaaaa
+cttccccatttttatctcatag--CCCAAACCCAAACCCAAACCCAAACCCAAgtaaaaa

extra/samples/sample2.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aCCCAAACCCAAACCCAAACCCAAACCCaa       
 >query
-cttccccatttttatctcatag-CCCAAACCCAAACCCAAACCCAAACCCaagtaaaaa
+cttccccatttttatctcatag-CCCAAACCCAAACCCAAACCCAAACCCAAgtaaaaa

extra/samples/sample3.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCCAAACCCAAACCCAAACCCAAACCCaa       
 >query
-cttccccatttttatctcatagacCCCAAACCCAAACCCAAACCCAAACCC--gtaaaaa
+cttccccatttttatctcatagACCCCAAACCCAAACCCAAACCCAAACCC--gtaaaaa

extra/samples/sample4.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCC
 >query
-cttccccatttttatctcatagac------------------------------------------------------------------------CCC------------------------------
+cttccccatttttatctcatagAC------------------------------------------------------------------------CCC------------------------------

extra/samples/sample5.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCTAAACCCAAACCCAAACCC
 >query
-cttccccatttttatctcatagacCCT------------------
+cttccccatttttatctcatagACCCT------------------

extra/samples/sample6.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCCAAACCCAAACCCAAACCCAAACCCaa       
 >query
-cttccccatttttatctcatagacCCCAAA-CCAAACCCAAACCCAAACCCaagtaaaaa
+cttccccatttttatctcatagACCCCAAA-CCAAACCCAAACCCAAACCCAAgtaaaaa

src/Alignment.c

@@ -25,12 +25,12 @@
 bool find_best_deletion(struct State* deletion, struct EmissionTable* emission_table, Literal* reference, Literal* query, char* result) {
 
   double prob=LOGODD_NEGINF, highest_prob=LOGODD_NEGINF;
-  uint_fast8_t best_pos=0, pos=0;
+  uint_fast16_t best_pos=0, pos=0;
   Literal lookup_query[3];
 
   if (deletion->num_emissions == 2) {
     for(; pos < 3; pos++) {
-      for (uint_fast8_t i=0; i < 3; i++) {
+      for (uint_fast16_t i=0; i < 3; i++) {
         if (pos == i) {
           lookup_query[i] = LITERAL_N;
           continue;
@@ -47,7 +47,7 @@ bool find_best_deletion(struct State* deletion, struct EmissionTable* emission_t
       prob = EmissionTable__by_literals(emission_table, reference, lookup_query);
       if (prob >= highest_prob) {
         highest_prob = prob;
-        for (uint_fast8_t j=0; j < 3; j++) {
+        for (uint_fast16_t j=0; j < 3; j++) {
           result[j] = Literal__char(lookup_query[j]);
         }
         result[pos] = '-';
@@ -63,7 +63,7 @@ bool find_best_deletion(struct State* deletion, struct EmissionTable* emission_t
   } else if (deletion->num_emissions == 1) {
     strncpy(result, "---", 3);
     for(; pos < 3; pos++) {
-      for (uint_fast8_t i=0; i < 3; i++) {
+      for (uint_fast16_t i=0; i < 3; i++) {
         if (pos == i) {
           lookup_query[i] = query[0];
         } else {
@@ -97,14 +97,14 @@ bool find_best_deletion(struct State* deletion, struct EmissionTable* emission_t
  * @param path the Viterbi path.
  * @return the alignment.
  */
-struct Alignment* Alignment__create(struct Fasta* fasta, uint8_t query_id, struct Params* params, size_t path_length, struct State** path) {
-  uint8_t reference_id = 0;
+struct Alignment* Alignment__create(struct Fasta* fasta, uint16_t query_id, struct Params* params, size_t path_length, struct State** path) {
+  uint16_t reference_id = 0;
   const char lower = 'a' - 'A';
   int numAlignedRefChars = 0;		/* for sanity check that the entire reference seq is contained in the alignment */
 
   struct Alignment* self = (struct Alignment*) SAFEMALLOC(sizeof(struct Alignment));
   size_t length = fasta->queries[query_id]->length;
-  for (uint8_t ref_id=0; ref_id < fasta->num_references; ref_id++) {
+  for (uint16_t ref_id=0; ref_id < fasta->num_references; ref_id++) {
     length += fasta->references[ref_id]->length;
   }
   self->reference = (char*) SAFECALLOC(sizeof(char), length+1+20*fasta->num_references);
@@ -114,10 +114,10 @@ struct Alignment* Alignment__create(struct Fasta* fasta, uint8_t query_id, struc
   char* deletion;
   char bases[4] = "";
 
-  uint_fast8_t pending_deletion=0;
+  uint_fast16_t pending_deletion=0;
   size_t q = 0, r = 0, t = 0;
   for (size_t i=1; i < path_length; i++) {
-    uint8_t j=0, emissions = path[i]->num_emissions;
+    uint16_t j=0, emissions = path[i]->num_emissions;
 
     // deleting 1nt and 2nt will always emit 3 bases/dashes to maintain reading frame intact.
     if (!strncmp("delete_1nt", path[i]->name, 10) || !strncmp("delete_2nt", path[i]->name, 10)) {
@@ -281,7 +281,7 @@ struct Alignment* Alignment__create(struct Fasta* fasta, uint8_t query_id, struc
 
   /* sanity check that the entire reference seq is contained in the alignment */
   int totalRefLen = 0;
-  for (uint8_t i=0; i < fasta->num_references; i++) {
+  for (uint16_t i=0; i < fasta->num_references; i++) {
       totalRefLen += fasta->references[i]->length;
   }
   if (numAlignedRefChars != totalRefLen) {

src/Alignment.h

@@ -17,7 +17,7 @@ typedef struct Alignment {
   char* query;
 } Alignment;
 
-struct Alignment* Alignment__create(struct Fasta* fasta, uint8_t query_id, struct Params* params, size_t path_length, struct State** sequence);
+struct Alignment* Alignment__create(struct Fasta* fasta, uint16_t query_id, struct Params* params, size_t path_length, struct State** sequence);
 bool Alignment__destroy(struct Alignment* self);
 
 #endif  // ALIGNMENT_H_

src/Arguments.c

@@ -61,7 +61,7 @@ bool Arguments__read(int argc, char** argv, struct Params* parameters) {
     die("Insufficient number of arguments. Please provide at least an input file.");
   }
 
-  uint8_t num_input_files = 0;
+  uint16_t num_input_files = 0;
   int i = 1;  // [0] is the cesar binary itself.
   while (argv[i] && i < argc) {
     char* argument = argv[i];

src/Cesar.c

@@ -53,7 +53,7 @@ int main(int argc, char* argv[argc]) {
   logv(1, "prefix %s\n", prefix);
 
   /* load profiles for each reference exon */
-  for (uint8_t i=0; i < fasta.num_references; i++) {
+  for (uint16_t i=0; i < fasta.num_references; i++) {
     struct Sequence* reference = fasta.references[i];
 
     /* load acceptor or first codon profile */
@@ -161,15 +161,15 @@ int main(int argc, char* argv[argc]) {
   size_t rlength = 0;
   size_t qlength = 0;
   size_t qlength_max = 0;
-  for (uint8_t i=0; i < fasta.num_references; i++) {
+  for (uint16_t i=0; i < fasta.num_references; i++) {
     struct Sequence* reference = fasta.references[i];
     num_states += 6 + 6 * reference->num_codons + 1 + 2 + 2 + 22 + 6;  /* 22 and 6 for acc and donor states */
 
     logv(1, "Reference %u length: %lu", i, fasta.references[i]->length);
     logv(1, "Reference %u split codon lengths: %u %u", i, fasta.references[i]->start_split_length, fasta.references[i]->end_split_length);
     rlength += fasta.references[i]->length;
   }
-  for (uint8_t i=0; i < fasta.num_queries; i++) {
+  for (uint16_t i=0; i < fasta.num_queries; i++) {
     logv(1, "Query %u length: %lu", i, fasta.queries[i]->length);
     qlength += fasta.queries[i]->length;
     if (fasta.queries[i]->length > qlength_max) {
@@ -197,14 +197,14 @@ int main(int argc, char* argv[argc]) {
 
   if (g_loglevel >= 7) {
     char* tmp;
-    for (uint8_t i=0; i < fasta.num_references; i++) {
+    for (uint16_t i=0; i < fasta.num_references; i++) {
       tmp = SAFECALLOC(sizeof(char), SEQUENCENAMELENGTH + fasta.references[i]->length);
       Literal__str(fasta.references[i]->length, fasta.references[i]->sequence, tmp);
       logv(1, ">original %s\n%s", fasta.references[i]->name, tmp);
       free(tmp);
     }
 
-    for (uint8_t i=0; i < fasta.num_queries; i++) {
+    for (uint16_t i=0; i < fasta.num_queries; i++) {
       tmp = SAFECALLOC(sizeof(char), SEQUENCENAMELENGTH + fasta.queries[i]->length);
       Literal__str(fasta.queries[i]->length, fasta.queries[i]->sequence, tmp);
       logv(1, ">original %s\n%s", fasta.queries[i]->name, tmp);
@@ -222,10 +222,10 @@ int main(int argc, char* argv[argc]) {
     fclose(dotfile);
   }
 
-  for (uint8_t q=0; q < fasta.num_queries; q++) {
+  for (uint16_t q=0; q < fasta.num_queries; q++) {
 
     size_t length = 2*fasta.queries[q]->length;
-    for (uint8_t i=0; i < fasta.num_references; i++) {
+    for (uint16_t i=0; i < fasta.num_references; i++) {
       length += fasta.references[i]->length;
     }
 
@@ -246,7 +246,7 @@ int main(int argc, char* argv[argc]) {
   }
 
   HMM__destroy(hmm);
-  for (uint8_t i=0; i<fasta.num_references; i++) {
+  for (uint16_t i=0; i<fasta.num_references; i++) {
     if(acceptors[i] != NULL) {
       Profile__destroy(acceptors[i]);
     }

src/EmissionTable.c

@@ -82,7 +82,7 @@ bool EmissionTable__read(struct EmissionTable* self, char* filename) {
       // corresponds to the line number.
       if (i==0) {
         Literal* codon = (Literal*) SAFEMALLOC(sizeof(Literal) * self->num_literals);
-        for (uint8_t j=0; j < self->num_literals; j++) {
+        for (uint16_t j=0; j < self->num_literals; j++) {
           codon[j] = Literal__from_char(token[j]);
         }
 
@@ -121,7 +121,7 @@ bool EmissionTable__set(struct EmissionTable* self, Literal sequence[], LOGODD_T
   bool result = true;
   // for each query, set logodd concerning 
   EMISSION_ID_T row = Literal__uint(self->num_literals, sequence);
-  for (uint8_t column=0; column < pow(4, self->num_literals); column++) {
+  for (uint16_t column=0; column < pow(4, self->num_literals); column++) {
     result &= LogoddMatrix__set(self->values, column, row, logodd);
     if (!result) {
       break;
@@ -143,7 +143,7 @@ bool EmissionTable__forbid(struct EmissionTable* self, Literal sequence[]) {
 /**
  * Recursively check for Ns in query and replace them by A,C,T,G while recording those in visited.
  */
-void EmissionTable__variants(uint8_t num_literals, Literal query[num_literals], uint8_t position, bool visited[]) {
+void EmissionTable__variants(uint16_t num_literals, Literal query[num_literals], uint16_t position, bool visited[]) {
   if (g_loglevel >= 6) {
     char tmp[4] = "";
     Literal__str(num_literals, query, tmp);
@@ -160,7 +160,7 @@ void EmissionTable__variants(uint8_t num_literals, Literal query[num_literals],
   }
 
   Literal copy[4];
-  for (uint8_t i=0; i < num_literals; i++) {
+  for (uint16_t i=0; i < num_literals; i++) {
     copy[i] = query[i];
   }
 
@@ -178,8 +178,8 @@ void EmissionTable__variants(uint8_t num_literals, Literal query[num_literals],
  * @return the probability to emit query.
  */
 LOGODD_T EmissionTable__by_literals(struct EmissionTable* self, Literal reference[], Literal query[]) {
-  uint8_t reference_Ns = Literal__Ns(self->num_literals, reference);
-  uint8_t query_Ns = Literal__Ns(self->num_literals, query);
+  uint16_t reference_Ns = Literal__Ns(self->num_literals, reference);
+  uint16_t query_Ns = Literal__Ns(self->num_literals, query);
 
   if (query_Ns == 0 && reference_Ns == 0) {
     EMISSION_ID_T row = Literal__uint(self->num_literals, reference);
@@ -199,7 +199,7 @@ LOGODD_T EmissionTable__by_literals(struct EmissionTable* self, Literal referenc
   bool* visited_reference = (bool*) SAFECALLOC(sizeof(bool), self->values->num_columns);
   EmissionTable__variants(self->num_literals, reference, 0, visited_reference);
 
-  uint8_t reference_visits = 0;
+  uint16_t reference_visits = 0;
   double total_sum = 0;
   for (EMISSION_ID_T row = 0; row < self->values->num_rows; row++) {
 
@@ -211,7 +211,7 @@ LOGODD_T EmissionTable__by_literals(struct EmissionTable* self, Literal referenc
     bool* visited_query = (bool*) SAFECALLOC(sizeof(bool), self->values->num_columns);
     EmissionTable__variants(self->num_literals, query, 0, visited_query);
 
-    uint8_t query_visits = 0;
+    uint16_t query_visits = 0;
     double sum = 0;
     for (EMISSION_ID_T column = 0; column < self->values->num_columns; column++) {
       if (!visited_query[column]) {
@@ -271,14 +271,14 @@ bool EmissionTable__init(struct EmissionTable* self, EMISSION_ID_T num_emissions
  * @param codons an array of a series of codons (e.g. [TAATGATAG] for all stop codons).
  * @return success boolean.
  */
-bool EmissionTable__init_single_codons(struct EmissionTable* self, uint8_t num_codons, Literal codons[num_codons]) {
+bool EmissionTable__init_single_codons(struct EmissionTable* self, EMISSION_ID_T num_codons, Literal codons[num_codons]) {
   EmissionTable__init(self, 3, LAMBDA_DISTRIBUTION);
   LOGODD_T one_nth = 1.0 - Logodd__log((double) num_codons);
 
-  for(uint8_t i = 0; i < num_codons; i++) {
+  for(uint16_t i = 0; i < num_codons; i++) {
     // for each query, set logodd concerning 
     EMISSION_ID_T row = Literal__uint(self->num_literals, &codons[3*i]);
-    for (uint8_t j = 0; j < num_codons; j++) {
+    for (uint16_t j = 0; j < num_codons; j++) {
       EMISSION_ID_T column = Literal__uint(self->num_literals, &codons[3*j]);
       if (! LogoddMatrix__set(self->values, column, row, one_nth)) {
         return false;
@@ -324,7 +324,7 @@ bool EmissionTable__str(struct EmissionTable* self, char buffer[]) {
 
 bool EmissionTable__emittable(struct EmissionTable* self, EMISSION_ID_T row) {
   bool emittable = false;
-  uint8_t column = 0;
+  uint16_t column = 0;
   while (column < self->values->num_columns && !emittable) {
     emittable = EmissionTable__get(self, column++, row) != LOGODD_NEGINF;
   }

src/EmissionTable.h

@@ -16,7 +16,7 @@
 typedef struct EmissionTable {
   LogoddMatrix* values;
   Distribution distribution;
-  uint8_t num_literals;
+  uint16_t num_literals;
 } EmissionTable;
 
 
@@ -27,7 +27,7 @@ bool EmissionTable__init_single_codons(struct EmissionTable* self, EMISSION_ID_T
 bool EmissionTable__destroy(struct EmissionTable* self);
 bool EmissionTable__set(struct EmissionTable* self, Literal sequence[], LOGODD_T logodd);
 bool EmissionTable__forbid(struct EmissionTable* self, Literal sequence[]);
-LOGODD_T EmissionTable__get(struct EmissionTable* self, uint_fast8_t column, uint_fast8_t row);
+LOGODD_T EmissionTable__get(struct EmissionTable* self, uint_fast16_t column, uint_fast16_t row);
 bool EmissionTable__str(struct EmissionTable* self, char buffer[]);
 bool EmissionTable__emittable(struct EmissionTable* self, EMISSION_ID_T reference);
 

src/Fasta.c

@@ -40,12 +40,12 @@ bool Fasta__init(struct Fasta* self) {
  * @return success boolean.
  */
 bool Fasta__destroy(struct Fasta* self) {
-  for(uint8_t i = 0; i < self->num_references; i++) {
+  for(uint16_t i = 0; i < self->num_references; i++) {
     Sequence__destroy(self->references[i]);
   }
   free(self->references);
 
-  for(uint8_t i = 0; i < self->num_queries; i++) {
+  for(uint16_t i = 0; i < self->num_queries; i++) {
     Sequence__destroy(self->queries[i]);
   }
   free(self->queries);
@@ -103,10 +103,10 @@ bool Fasta__read(struct Fasta* self, char* filename) {
   struct Sequence* sequence = SAFECALLOC(sizeof(Sequence), 1);
   Sequence__init(sequence);
 
-  uint8_t name_length = 0;
-  uint8_t acc_length = 0;
-  uint8_t do_length = 0;
-  uint8_t state = 0;
+  uint16_t name_length = 0;
+  uint16_t acc_length = 0;
+  uint16_t do_length = 0;
+  uint16_t state = 0;
   size_t lineno = 0;
   bool reached_codons = false;
   bool reached_queries = false;

src/Fasta.h

@@ -12,8 +12,8 @@
 #include "Sequence.h"
 
 typedef struct Fasta {
-  uint8_t num_references;
-  uint8_t num_queries;
+  uint16_t num_references;
+  uint16_t num_queries;
   struct Sequence** references;
   struct Sequence** queries;
 } Fasta;