Update docs, help, and change name to synder

.gitignore

@@ -1,5 +1,4 @@
-synfull
-run
+synder
 
 README.pdf
 

Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = "Fagin"
+PROJECT_NAME           = "Synder"
 PROJECT_NUMBER         =
 PROJECT_BRIEF          =
 PROJECT_LOGO           =

Makefile

@@ -1,4 +1,4 @@
-TARGET=run
+TARGET=synder
 
 all:
 	cd src && ${MAKE}

README.md

@@ -1,7 +1,7 @@
 # Manual stub
 
 #Contiguous Set Use
-./run -i GFF -s DB -c contig
+./synder -i GFF -s DB -c contig
 
 output is like -c map with additon of flag
 SEQNAME TARGETNAME SEARCH_INTERVAL_START SEARCH_INTERVAL_STOP FLAG
@@ -60,8 +60,8 @@ of the syntenic blocks, will always be considered "syntenically scrambled".
 
 # TODO list for version 1
 
- - [ ] Implement the query context to contiguous function
- - [ ] Implement the contiguous set to search interval function
+ - [x] Implement the query context to contiguous function
+ - [x] Implement the contiguous set to search interval function
  - [ ] Clean up the CLI user interface
  - [ ] Specify the synteny class (A-F) of the output search intervals 
 

src/Makefile

@@ -1,6 +1,6 @@
 CFLAGS=-Wall -g -O2
 CC=gcc
-TARGET=run
+TARGET=synder
 OBJECTS=main.o test.o io.o genome.o analysis.o contig.o interval.o itree.o search.o ia.o iv.o block.o synmap.o ui.o contiguous.o
 
 ${TARGET}: ${OBJECTS}

src/main.c

@@ -65,7 +65,7 @@ int main(int argc, char * argv[]){
         else if(strcmp(args.cmd, "map") == 0){
 	        analysis_map(syn, args.intfile);
         }
-        else if(strcmp(args.cmd, "contig") ==0){
+        else if(strcmp(args.cmd, "search") ==0){
        		contiguous_query(syn, args.intfile);   
 		}
         else{

src/ui.c

@@ -34,12 +34,13 @@ void close_Arguments(Arguments arg){
         fclose(arg.hitfile);
     if(arg.db_filename)
         free(arg.db_filename);
-    if(arg.pos)
+    if(arg.pos){
         for(int i = 0; i < 3; i++){
             if(arg.pos[i])
                 free(arg.pos[i]);
         }
         free(arg.pos);
+    }
     if(arg.cmd)
         free(arg.cmd);
 }
@@ -57,19 +58,21 @@ void check_file(FILE * fp, char * name){
 
 void print_help(){
     printf(
-    "USAGE: synfull -d SYNTENY_FILE QUERY TARGET DEST_DIR\n"
-    "USAGE: synfull -i GFF_FILE -s SYNTENY_DB\n"
+    "USAGE\n"
+    "  synder -d SYNTENY_FILE QUERY TARGET DB_DIR\n"
+    "  synder [OPTIONS] -s SYNTENY_DB -c COMMAND\n"
     "COMMANDS\n"
-    "map    - print target intervals overlapping each query interval\n"
-    "count  - like map but prints only the number that overlap\n"
-    "filter - print query-to-target links consistent with the synteny map\n"
-    "pred   - predict target search spaces for each query interval\n"
-    "EXAMPLES:\n"
-    "$ synfull -d at-al.tab at al db\n"
-    "$ synfull -i at.gff -s db/at_al.txt -c count\n"
-    "$ synfull -i at.gff -s db/at_al.txt -c map\n"
-    "$ synfull -f hits.syn -s db/at_al.txt -c filter\n"
-    "$ synfull test\n"
+    "  map    - print target intervals overlapping each query interval\n"
+    "  count  - like map but prints only the number that overlap\n"
+    "  search - find target search spaces for each query interval\n"
+    "  filter - print query-to-target links consistent with the synteny map\n"
+    "EXAMPLES\n"
+    "  synder -d at-al.tab at al db\n"
+    "  synder -i at.gff   -s db/at_al.txt -c map\n"
+    "  synder -i at.gff   -s db/at_al.txt -c count\n"
+    "  synder -i at.syn   -s db/at_al.txt -c search\n"
+    "  synder -f hits.syn -s db/at_al.txt -c filter\n"
+    "  synder test\n"
     );
     exit(EXIT_SUCCESS);
 }