Merge pull request #31 from calico/thread-1hot

1-hot encode in parallel

src/baskerville/snps.py

@@ -164,10 +164,20 @@ def score_write(ref_preds, alt_preds, si):
     si = 0
 
     with concurrent.futures.ThreadPoolExecutor() as executor:
-        for sc in tqdm(snp_clusters):
-            snp_1hot_list = sc.get_1hots(genome_open)
+        # initialize 1 hot encoding
+        sc0 = snp_clusters[0]
+        s1l = executor.submit(sc0.get_1hots, genome_open)
+
+        for ci, sc in enumerate(tqdm(snp_clusters)):
+            # pull latest 1 hot encoding
+            snp_1hot_list = s1l.result()
             ref_1hot = np.expand_dims(snp_1hot_list[0], axis=0)
 
+            # submit next 1 hot encoding
+            if ci + 1 < len(snp_clusters):
+                sc1 = snp_clusters[ci + 1]
+                s1l = executor.submit(sc1.get_1hots, genome_open)
+
             # predict reference
             ref_preds = []
             for shift in options.shifts: