fix: now properly sort arrays with inline functions

2 files changed, 36 insertions, 12 deletions

diff --git a/sys/libbio/align.c b/sys/libbio/align.c
index bcb6fd3..8d1c119 100644
--- a/sys/libbio/align.c
+++ b/sys/libbio/align.c
@@ -1,5 +1,6 @@
 #include <u.h>
 #include <libn.h>
+#include <libn/macro/qsort.h>
 #include <libbio.h>
 
 // -----------------------------------------------------------------------
@@ -70,6 +71,22 @@ murmurhash(uint64 x, uint64 mask)
 // -----------------------------------------------------------------------
 // Locality sensitive hashing (with spatial extent)
 
+static
+void
+sortpos(uintptr len, uint64 vals[], int locs[])
+{
+    int    tmpi;
+    uint64 tmpu64;
+
+#define LESS(i, j) (locs[i] < locs[j])
+#define SWAP(i, j) (tmpu64  = vals[i], tmpi    = locs[i], \
+                    vals[i] = vals[j], locs[i] = locs[j], \
+                    vals[j] = tmpu64 , locs[j] = tmpi)
+        QSORT(len, LESS, SWAP);
+#undef LESS
+#undef SWAP
+}
+
 error
 aln·sketch(byte *seq, int L, uint64 *vals[aln·N], int *locs[aln·N])
 {
@@ -113,32 +130,39 @@ aln·sketch(byte *seq, int L, uint64 *vals[aln·N], int *locs[aln·N])
         }
     }
 
-    // TODO: Sort vals by their locs
+    for (n = 0; n < aln·N; n++) {
+        sortpos(L, vals[n], locs[n]);
+    }
     
     return 0;
 }
 
 static
 int
-compare(void *a, void *b)
+cmparrs(int L, uint64 a[], uint64 b[])
 {
     int l;
-    uint64 *a64, *b64;
 
-    a64 = (uint64*)a;
-    b64 = (uint64*)b;
-    for (l = 0; l < aln·L; l++) {
-        if (a64 < b64) return -1;
-        if (a64 > b64) return +1;
+    for (l = 0; l < L; l++) {
+        if (a[l] < b[l]) return -1;
     }
 
-    return 0;
+    return +1;
 }
 
 // TODO: replace with inlined version
 error
-aln·sort(int len, int l, uint64 *vals)
+aln·sort(uintptr len, int L, uint64 *vals)
 {
-    qsort(vals, len, l*sizeof(uint64), &compare);
+    uint64 tmp[128];
+#define LESS(i, j) (cmparrs((L), (vals+(i)*L), (vals+(j)*L)))
+#define SWAP(i, j) (memcpy(tmp, (vals+(i)*L), (sizeof(uint64)*L)),     \
+                    memcpy((vals+(i)*L), (vals+(j)*L), (sizeof(uint64)*L)), \
+                    memcpy((vals+(j)*L), tmp,  (sizeof(uint64)*L)))
+       
+    QSORT(len, LESS, SWAP);
+#undef LESS
+#undef SWAP
+    // qsort(vals, len, l*sizeof(uint64), &compare);
     return 0;
 }
diff --git a/sys/libbio/test.c b/sys/libbio/test.c
index fec0a0c..aa14382 100644
--- a/sys/libbio/test.c
+++ b/sys/libbio/test.c
@@ -241,7 +241,7 @@ main()
         for (i = 0; i < arrlen(SEQ); i++) {
             printf("[");
             for (l = 0; l < aln·L; l++) {
-                printf("%d,", loc[n][i][l]);
+                printf("%lu,", mem[n][i][l]);
             }
             printf("]");
             if (i == 0) printf(" ~ ");