commit mig her

Author: Your Name

shared.cpp

@@ -14,60 +14,6 @@
 #include <map>      // for operator!=, __map_iterator, operator==
 #include <vector>   // for vector
 
-static int decode_nt16_acgt(uint8_t nt16) {
-    if (nt16 == 1) return 0; // A
-    if (nt16 == 2) return 1; // C
-    if (nt16 == 4) return 2; // G
-    if (nt16 == 8) return 3; // T
-    return -1;
-}
-
-double dust_score_nt16(const uint8_t *seq, int32_t l, int32_t window) {
-    const int32_t WLEN = 3;
-    const int32_t WTOT = 64;
-    const int32_t WMASK = WTOT - 1;
-    if (window < WLEN || window > 64)
-        return -1.0;
-
-    int32_t wCount[WTOT];
-    int32_t wSeq[64];
-    memset(wCount, 0, sizeof(wCount));
-    memset(wSeq, 0, sizeof(wSeq));
-
-    int64_t score = 0;
-    int64_t maxScore = 0;
-    int32_t t = 0;
-    int32_t n = -WLEN;
-
-    for (int32_t i = 0; i < l; ++i) {
-        const int b = decode_nt16_acgt(bam_seqi(seq, i));
-        if (b < 0)
-            continue; // ignore N/ambiguous
-
-        t = ((t << 2) | b) & WMASK;
-        if (++n >= 0) {
-            const int32_t k = n % window;
-            if (n >= window) {
-                const int32_t x = wSeq[k];
-                if (wCount[x] > 0)
-                    score -= --wCount[x];
-                score += wCount[t]++;
-                if (score > maxScore)
-                    maxScore = score;
-            } else {
-                score += wCount[t]++;
-            }
-            wSeq[k] = t;
-        }
-    }
-
-    if (n <= 0)
-        return 0.0;
-    if (n >= window)
-        return (200.0 * (double)maxScore) / (window * (window - 1));
-    return (200.0 * (double)score) / (n * (n + 1));
-}
-
 
 int file_is_older(const char *file1, const char *file2) {
     struct stat st1, st2;

test/testAll2.sh

@@ -116,9 +116,14 @@ test_dust_unit() {
     local unit_src="test_dust_score.cpp"
     local unit_bin="output/test_dust_score_unit"
 
+    # Build the shared dust-score object via top-level make rules so include/link
+    # settings match the main build (works with both bundled and system htslib).
+    run_logged "Building dust score object" \
+        make -C .. dust_score.o
+
     run_logged "Compiling dust unit test" \
-        c++ -O2 -Wall -Wextra -I.. "${unit_src}" ../shared.o \
-        -o "${unit_bin}" -lz -lm -lpthread -lhts
+        c++ -O2 -Wall -Wextra -I.. "${unit_src}" ../dust_score.o \
+        -o "${unit_bin}"
 
     if [[ -x "${unit_bin}" ]]; then
         run_logged "Running dust unit test" "${unit_bin}"