Release v0.12.1 - clean build

Makefile

@@ -62,8 +62,9 @@ dtest-leak:
 .PHONY: dclean
 dclean:
 	rm -f vgcore.* gmon.out *log valgrind*
-	rm -rf zzz* db [a-z] gdb.txt ark
+	rm -rf zzz* db [a-z] gdb.txt ark .gdb_cmds
 	rm -f expected-output gdb input.gff observed-output synteny-map.tab
+	rm -f synmap.txt
 
 
 # Runs the sample data, linking files for review

src/Makefile

@@ -1,13 +1,14 @@
-# CFLAGS=-Wall -g -std=gnu99 -lm
-# CFLAGS=-Wall -g -std=gnu99 -lm -m64
-CFLAGS=-Wall -gdwarf-4 -g3 -std=gnu99 -lm
+# CFLAGS=-Wall -g -std=gnu99
+# CFLAGS=-Wall -g -std=gnu99 -m64
+CFLAGS=-Wall -gdwarf-4 -g3 -std=gnu99
+LINKER_FLAGS=-lm
 CC=gcc
 TARGET=synder
 
 OBJECTS=ia.o iv.o interval.o itree.o search.o ui.o lev.o block.o contig.o genome.o contiguous_set.o synmap.o io.o analysis.o map.o main.o global.o
 
 ${TARGET}: ${OBJECTS}
-	${CC} -o ${TARGET} ${CFLAGS} ${OBJECTS}
+	${CC} -o ${TARGET} ${OBJECTS} ${LINKER_FLAGS}
 
 global.o: global.c global.h
 	${CC} -c ${CFLAGS} global.[ch]

src/block.c

@@ -5,7 +5,7 @@ void set_Block(
     Block*  block,
     long    start,
     long    stop,
-    float   score,
+    double   score,
     char    strand,
     Contig* parent,
     Block*  over,
@@ -117,9 +117,9 @@ void merge_block_a_into_b(Block * a, Block * b){
     long olen = overlap_length(a, b);
     long al = a->pos[1] - a->pos[0] + 1;
     long bl = b->pos[1] - b->pos[0] + 1;
-    float score =
-        ((float)(al - olen) / (al)) * a->score +
-        ((float)(bl - olen) / (bl)) * b->score +
+    double score =
+        ((double)(al - olen) / (al)) * a->score +
+        ((double)(bl - olen) / (bl)) * b->score +
         olen * (a->score / al + b->score / bl) / 2;
 
     b->score = score;

src/block.h

@@ -10,7 +10,7 @@ void set_Block(
     Block*  block,
     long    start,
     long    stop,
-    float   score,
+    double   score,
     char    strand,
     Contig* parent,
     Block*  over,

src/global.h

@@ -1,16 +1,16 @@
 #ifndef __GLOBAL_H__
 #define __GLOBAL_H__
 
+#include <math.h>
 #include <errno.h>
 #include <stdlib.h>
 #include <stdio.h>
 #include <stdbool.h>
 #include <string.h>
+#include <stdint.h>
 #include <errno.h>
 #include <limits.h>
 #include <assert.h>
-#include <math.h>
-
 
 #define REL_GT(x, y, d)   ((d) ? (x) >  (y) : (x) <  (y))
 #define REL_LT(x, y, d)   ((d) ? (x) <  (y) : (x) >  (y))
@@ -151,7 +151,7 @@ struct Block {
   Block         *cnr[2]; // adjacent block in contiguous set
   ContiguousSet *cset;   // contiguous set id
   long          pos[2];  // start and stop positions
-  float         score;   // score provided by synteny program
+  double         score;   // score provided by synteny program
   size_t        grpid;   // overlapping group id;
   char          strand;  // strand [+-.]
   size_t        linkid;  // a unique block id used mostly for debugging

src/io.c

@@ -1,4 +1,3 @@
-#include "global.h"
 #include "io.h"
 
 void check_args(size_t line_no, size_t nargs, size_t correct_nargs);
@@ -56,7 +55,7 @@ Synmap *load_Synmap(FILE * synfile, int swap, long k, char trans)
   line_no = 0;
   size_t qcon_id, qblk_id, tcon_id, tblk_id;
   long qstart, qstop, tstart, tstop;
-  float score;
+  double score;
   char strand;
 
   Block *qblk, *tblk;
@@ -67,7 +66,7 @@ Synmap *load_Synmap(FILE * synfile, int swap, long k, char trans)
     if (line[0] != '$')
       continue;
     unloaded_blocks -= 2;
-    status = sscanf(line, "$ %zu %zu %zu %zu %zu %zu %zu %zu %f %c %c\n",
+    status = sscanf(line, "$ %zu %zu %zu %zu %zu %zu %zu %zu %lf %c %c\n",
                     &qcon_id, &qblk_id, &qstart, &qstop,
                     &tcon_id, &tblk_id, &tstart, &tstop, &score, &strand, &dummy);
     check_args(line_no, status, 10);

src/itree/ia.c

@@ -1,7 +1,4 @@
-#include <stdlib.h>
-
 #include "ia.h"
-#include "interval.h"
 
 IA * init_IA(){
     IA * ia = (IA *)malloc(sizeof(IA));

src/itree/interval.c

@@ -1,6 +1,3 @@
-#include <stdlib.h>
-#include <stdio.h>
-
 #include "interval.h"
 
 Interval * init_Interval(long start, long stop){

src/itree/interval.h

@@ -1,6 +1,7 @@
 #ifndef __INTERVAL_H__
 #define __INTERVAL_H__
 
+#include <stdio.h>
 #include <stdlib.h>
 
 /** the eponymous structure */

src/itree/itree.c

@@ -1,13 +1,4 @@
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <assert.h>
-#include <stdbool.h>
-
 #include "itree.h"
-#include "interval.h"
-#include "ia.h"
-#include "iv.h"
 
 /* local function prototypes */
 IntervalTree * build_tree_r(IA * intervals, IntervalTree * parent, Orientation orientation);

src/itree/itree.h

@@ -1,8 +1,15 @@
 #ifndef __ITREE_H__
 #define __ITREE_H__
 
-#include "ia.h"
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <stdbool.h>
+
 #include "interval.h"
+#include "ia.h"
+#include "iv.h"
 
 typedef enum orientation {
     O_LEFT = -1,

src/itree/iv.c

@@ -1,9 +1,3 @@
-#include <stdlib.h>
-#include <string.h>
-#include <stdbool.h>
-#include <stdio.h>
-#include <assert.h>
-
 #include "iv.h"
 
 IV * init_IV(size_t available){

src/itree/iv.h

@@ -3,10 +3,12 @@
 
 #define IV_INITIAL_SIZE 8
 
+#include <string.h>
+#include <stdio.h>
+#include <assert.h>
 #include <stdlib.h>
 #include <stdbool.h>
 
-
 #include "interval.h"
 #include "ia.h"
 

src/itree/search.c

@@ -1,11 +1,4 @@
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <assert.h>
-#include <stdbool.h>
-
 #include "search.h"
-#include "iv.h"
 
 long count_interval_overlaps_r(Interval *, IntervalTree *, long);
 long count_point_overlaps_r(long, IntervalTree *, long);

src/itree/search.h

@@ -1,10 +1,13 @@
 #ifndef __SEARCH_H__
 #define __SEARCH_H__
 
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
 #include <stdbool.h>
 
 #include "ia.h"
-#include "iv.h"
 #include "interval.h"
 #include "itree.h"
 

src/lev.c

@@ -1,9 +1,3 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdint.h>
-#include <stdbool.h>
-
 #include "lev.h"
 
 void convert_seqname(FILE * synfile, FILE * intfile, int swap)

src/lev.h

@@ -1,8 +1,6 @@
 #ifndef __LEV_H__
 #define __LEV_H__
 
-#include <stdint.h>
-
 #include "global.h"
 
 #define TOLC(s)	for(char *p =(s);*p;++p) *p=*p>0x40&&*p<0x5b?*p|0x60:*p

src/map.c

@@ -1,6 +1,4 @@
 #include "map.h"
-#include "contig.h"
-#include "synmap.h"
 
 // A local utility structure used filter and store contiguous sets
 typedef struct CSList{
@@ -55,7 +53,7 @@ void find_search_intervals(Synmap * syn, FILE * intfile, bool pblock)
   // Row output of ctree
   ResultContig * crc;
   // Search interval score
-  float score;
+  double score;
 
   char *line = (char *) malloc(LINE_BUFFER_SIZE * sizeof(char));
   while (fgets(line, LINE_BUFFER_SIZE, intfile) && !feof(intfile)) {
@@ -107,7 +105,7 @@ void find_search_intervals(Synmap * syn, FILE * intfile, bool pblock)
         get_si_bound(bounds[HI], set_bounds, blk_bounds, HI, inverted);
 
 
-      printf("%s\t%s\t%zu\t%zu\t%s\t%zu\t%zu\t%c\t%f\t%zu\t%i\t%i\t%i\n",
+      printf("%s\t%s\t%zu\t%zu\t%s\t%zu\t%zu\t%c\t%lf\t%zu\t%i\t%i\t%i\n",
                                                          // Output column ids:
         seqname,                                         //  1
         blk_bounds[LO]->parent->name,                    //  2
@@ -274,7 +272,7 @@ SI_Bound * get_si_bound(
 //      |===|    |             |                 |===|
 //      |<------>| far         |       near |<-->|
 //          |<-->| near        |        far |<------>|
-float _flank_area(long near, long far, float k){
+double _flank_area(long near, long far, double k){
 
     // If far <= 0, this means there is no interval to score in this direction
     if(far > 0){
@@ -296,12 +294,12 @@ float _flank_area(long near, long far, float k){
     return 0;
 }
 
-float calculate_score(long a1, long a2, Block * blk){
+double calculate_score(long a1, long a2, Block * blk){
 
-    float weighted_length;
+    double weighted_length;
     long b1, b2, actual_length;
-    float k = 0.001;
-    float score = 0;
+    double k = 0.001;
+    double score = 0;
 
     if(blk == NULL)
         return score;

src/map.h

@@ -1,11 +1,11 @@
 #ifndef __MAP_H__
 #define __MAP_H__
 
-#include <stdint.h>
-
 #include "global.h"
 #include "block.h"
 #include "synmap.h"
+#include "contig.h"
+#include "synmap.h"
 
 #define ANCHORED  0
 #define BOUND     1
@@ -30,8 +30,8 @@
  */
 void find_search_intervals(Synmap * syn, FILE * intfile, bool pblock);
 
-float calculate_score(long start, long stop, Block * blk);
+double calculate_score(long start, long stop, Block * blk);
 
-float calculate_target_score(long a1, long a2, Block * bounds[2]);
+double calculate_target_score(long a1, long a2, Block * bounds[2]);
 
 #endif

src/synmap.c

@@ -1,7 +1,4 @@
-#include "global.h"
 #include "synmap.h"
-#include "contiguous_set.h"
-
 
 Synmap* init_Synmap()
 {

src/synmap.h

@@ -3,6 +3,8 @@
 
 #include "global.h"
 #include "genome.h"
+#include "global.h"
+#include "contiguous_set.h"
 
 /**
  * Allocate memory for a new Synmap.

src/ui.c

@@ -1,11 +1,7 @@
-#define _GNU_SOURCE
-#include <getopt.h>
-
-#include "global.h"
 #include "ui.h"
-#include "version.h"
 
-#define MAX_POS 5
+#define _GNU_SOURCE
+#include <getopt.h>
 
 /** contains all legal arguments from all subcommands */
 Arguments create_Arguments()

src/ui.h

@@ -2,6 +2,10 @@
 #define __UI_U__
 
 #include "global.h"
+#include "version.h"
+
+// maximum number of positional arguments
+#define MAX_POS 5
 
 /** Parsed command line arguments */
 typedef struct Arguments {

src/version.h

@@ -1,6 +1,6 @@
 #ifndef __VERSION_H__
 #define __VERSION_H__
 
-#define VERSION "v0.12.0"
+#define VERSION "v0.12.1"
 
 #endif