Merge pull request #180 from pangenome/update_seg_fault_abpoa

update `abpoa`
pangenome · Dec 8, 2022 · a8a0e9e · a8a0e9e
2 parents bd3f497 + e67ab35
commit a8a0e9e
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/deps/abPOA b/deps/abPOA
diff --git a/src/smooth.cpp b/src/smooth.cpp
@@ -276,7 +276,12 @@ odgi::graph_t* smooth_abpoa(const xg::XG &graph, const block_t &block, const uin
     //     if (seq_lens[i] > max_len) max_len = seq_lens[i];
     // }
 
-    abpoa_poa(ab, abpt, bseqs, seq_lens, exist_n_seq, n_seq);
+    int j, **weights = (int**)_err_malloc(n_seq * sizeof(int*));
+    for (i = 0; i < n_seq; ++i) {
+        weights[i] = (int*)_err_malloc(seq_lens[i] * sizeof(int));
+        for (j = 0; j < seq_lens[i]; ++j) weights[i][j] = 1;
+    }
+    abpoa_poa(ab, abpt, bseqs, weights, seq_lens, exist_n_seq, n_seq);
 
     // It seems not necessary, as the Breadth-First-Search (in build_odgi_abPOA) follows the graph topology
     //abpoa_topological_sort(ab->abg, abpt);
@@ -448,10 +453,11 @@ odgi::graph_t* smooth_abpoa(const xg::XG &graph, const block_t &block, const uin
     // free memory
     for (i = 0; i < n_seq; ++i) {
         free(bseqs[i]);
+        free(weights[i]);
     }
     free(bseqs);
     free(seq_lens);
-
+    free(weights);
     if (save_block_fastas) {
         std::chrono::duration<double> elapsed_time = std::chrono::steady_clock::now() - start_time;
         write_fasta_for_block(graph, block, block_id, seqs, names, "smoothxg_into_abpoa_pad" + std::to_string(poa_padding) + "_", "_in_" +  std::to_string(elapsed_time.count()) + "s");
+12 −13		README.md
+12 −4		example.c
+6 −5		include/abpoa.h
+7 −5		python/cabpoa.pxd
+1 −1		python/example.py
+4 −1		python/pyabpoa.pyx
+2 −2		setup.py
+8 −5		src/abpoa.c
+6 −5		src/abpoa.h
+52 −19		src/abpoa_align.c
+55 −28		src/abpoa_graph.c
+39 −37		src/abpoa_output.c
+8 −8		src/abpoa_seq.c
+7 −7		src/simd_abpoa_align.c
+1 −1		sub_example.c