Merge pull request #77 from SooLee/isoc99

Isoc99
4dn-dcic · Feb 2, 2024 · 94d0107 · 94d0107
2 parents ea19c74 + bfe81d1
commit 94d0107
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Showing 4 changed files with 81 additions and 80 deletions.
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-0.3.7
+0.3.8
diff --git a/src/pairix.h b/src/pairix.h
@@ -28,7 +28,7 @@
 #ifndef __TABIDX_H
 #define __TABIDX_H
 
-#define PACKAGE_VERSION "0.3.7"
+#define PACKAGE_VERSION "0.3.8"
 
 #include <stdint.h>
 #include "kstring.h"

diff --git a/src/pairs_merger.c b/src/pairs_merger.c
@@ -10,47 +10,6 @@
 
 #define FILENAMEMAX 2000
 
-int main(int argc, char *argv[])
-{
-    int num_fn = argc -1;
-    int i;
-    //BGZF *bzfp;
-    //int f_dst;
-
-    if(argc==1){
-       fprintf(stderr, "\n");
-       fprintf(stderr, "Program: pairs_merger\n");
-       fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
-       //fprintf(stderr, "Usage:   pairs_merger <in1.pairs.gz> <in2.pairs.gz> <in3.pairs.gz> ... > out.pairs.gz\n\n");
-       fprintf(stderr, "Usage:   pairs_merger <in1.pairs.gz> <in2.pairs.gz> <in3.pairs.gz> ... | bgzip -c  > out.pairs.gz\n\n");
-       return(1);
-    }
-
-    char *fn_list[num_fn];
-    for(i=0;i<num_fn;i++) {
-       fn_list[i]=malloc(FILENAMEMAX*sizeof(char));
-       strcpy(fn_list[i],argv[i+1]);
-    }
-
-    // write to stdout bgzip
-    //f_dst = fileno(stdout);
-    //bzfp = bgzf_dopen(f_dst, "w");
-
-    // actually write merged pairs to bzfp stdout
-    //int res = pairs_merger(fn_list, num_fn, bzfp);
-    int res = pairs_merger(fn_list, num_fn, NULL);
-
-    // close bgzf stream
-    //if (bgzf_close(bzfp) < 0) fail(bzfp);
-    //if (bgzf_close(bzfp) < 0){  fprintf(stderr,"Error: %d\n",bzfp->errcode); return(1); }
-
-
-    for(i=0;i<num_fn;i++) {
-       free(fn_list[i]);
-    }
-    return(res);
-}
-
 int pairs_merger(char **fn, int n, BGZF *bzfp)  // pass bgfp if the result should be bgzipped. or pass NULL.
 {
     pairix_t *tbs[n];
@@ -91,6 +50,47 @@ int pairs_merger(char **fn, int n, BGZF *bzfp)  // pass bgfp if the result shoul
       for(i=0;i<n;i++) ti_close(tbs[i]);
       for(i=0;i<n_uniq_seq;i++) free(uniq_seq_list[i]);
       free(uniq_seq_list);
-      return(NULL);
-    } else { fprintf(stderr,"Null unique seq list\n"); return(NULL); }
+      return(0);
+    } else { fprintf(stderr,"Null unique seq list\n"); return(0); }
+}
+
+int main(int argc, char *argv[])
+{
+    int num_fn = argc -1;
+    int i;
+    //BGZF *bzfp;
+    //int f_dst;
+
+    if(argc==1){
+       fprintf(stderr, "\n");
+       fprintf(stderr, "Program: pairs_merger\n");
+       fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
+       //fprintf(stderr, "Usage:   pairs_merger <in1.pairs.gz> <in2.pairs.gz> <in3.pairs.gz> ... > out.pairs.gz\n\n");
+       fprintf(stderr, "Usage:   pairs_merger <in1.pairs.gz> <in2.pairs.gz> <in3.pairs.gz> ... | bgzip -c  > out.pairs.gz\n\n");
+       return(1);
+    }
+
+    char *fn_list[num_fn];
+    for(i=0;i<num_fn;i++) {
+       fn_list[i]=malloc(FILENAMEMAX*sizeof(char));
+       strcpy(fn_list[i],argv[i+1]);
+    }
+
+    // write to stdout bgzip
+    //f_dst = fileno(stdout);
+    //bzfp = bgzf_dopen(f_dst, "w");
+
+    // actually write merged pairs to bzfp stdout
+    //int res = pairs_merger(fn_list, num_fn, bzfp);
+    int res = pairs_merger(fn_list, num_fn, NULL);
+
+    // close bgzf stream
+    //if (bgzf_close(bzfp) < 0) fail(bzfp);
+    //if (bgzf_close(bzfp) < 0){  fprintf(stderr,"Error: %d\n",bzfp->errcode); return(1); }
+
+
+    for(i=0;i<num_fn;i++) {
+       free(fn_list[i]);
+    }
+    return(res);
 }
diff --git a/src/streamer_1d.c b/src/streamer_1d.c
@@ -10,41 +10,6 @@
 
 #define FILENAMEMAX 2000
 
-int main(int argc, char *argv[])
-{
-    //BGZF *bzfp;
-    //int f_dst;
-
-    if(argc==1){
-       fprintf(stderr, "\n");
-       fprintf(stderr, "Program: streamer_1d\n");
-       fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
-       fprintf(stderr, "Resorter (convert a file sorted by chr1-chr2-pos1-pos2 to a stream sorted by chr1-pos1)\n\n");
-       fprintf(stderr, "Usage:   streamer_1d in.2d.pairs.gz > out.1d.pairs\n");
-       fprintf(stderr, "Usage:   streamer_1d in.2d.pairs.gz | bgzip -c  > out.1d.pairs.gz\n\n");
-       return(1);
-    }
-
-    char *fn;
-    fn=malloc(FILENAMEMAX*sizeof(char));
-    strcpy(fn,argv[1]);
-
-    // write to stdout bgzip (This is slower, so don't use it)
-    //f_dst = fileno(stdout);
-    //bzfp = bgzf_dopen(f_dst, "w");
-
-    // actually write merged pairs to bzfp stdout
-    //int res = stream_1d(fn, bzfp);
-    int res = stream_1d(fn);
-
-    // close bgzf stream
-    //if (bgzf_close(bzfp) < 0) fail(bzfp);
-    //if (bgzf_close(bzfp) < 0){  fprintf(stderr,"Error: %d\n",bzfp->errcode); return(1); }
-
-    free(fn);
-    return(res);
-}
-
 
 // Uc->Up converter - convert a single 2D-sorted file into a 1D-sorted stream.
 int stream_1d(char *fn)
@@ -91,3 +56,39 @@ int stream_1d(char *fn)
 
     return (0);
 }
+
+int main(int argc, char *argv[])
+{
+    //BGZF *bzfp;
+    //int f_dst;
+
+    if(argc==1){
+       fprintf(stderr, "\n");
+       fprintf(stderr, "Program: streamer_1d\n");
+       fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
+       fprintf(stderr, "Resorter (convert a file sorted by chr1-chr2-pos1-pos2 to a stream sorted by chr1-pos1)\n\n");
+       fprintf(stderr, "Usage:   streamer_1d in.2d.pairs.gz > out.1d.pairs\n");
+       fprintf(stderr, "Usage:   streamer_1d in.2d.pairs.gz | bgzip -c  > out.1d.pairs.gz\n\n");
+       return(1);
+    }
+
+    char *fn;
+    fn=malloc(FILENAMEMAX*sizeof(char));
+    strcpy(fn,argv[1]);
+
+    // write to stdout bgzip (This is slower, so don't use it)
+    //f_dst = fileno(stdout);
+    //bzfp = bgzf_dopen(f_dst, "w");
+
+    // actually write merged pairs to bzfp stdout
+    //int res = stream_1d(fn, bzfp);
+    int res = stream_1d(fn);
+
+    // close bgzf stream
+    //if (bgzf_close(bzfp) < 0) fail(bzfp);
+    //if (bgzf_close(bzfp) < 0){  fprintf(stderr,"Error: %d\n",bzfp->errcode); return(1); }
+
+    free(fn);
+    return(res);
+}
+