add put_gap_at_end; bugs in sub_aln & n_span_read

yangao07 · Jan 28, 2025 · c8d6f99 · c8d6f99
1 parent 6670bbe
commit c8d6f99
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/include/abpoa.h b/include/abpoa.h
@@ -78,7 +78,7 @@ typedef struct {
     // alignment mode
     uint8_t ret_cigar:1, rev_cigar:1, out_msa:1, out_cons:1, out_gfa:1, out_fq:1, use_read_ids:1, amb_strand:1;
     // sub_aln: reads align to subgraph, total read count is based on subgraph coverage, i.e., node.n_span_read, not total input read count
-    uint8_t sub_aln:1, use_qv:1, disable_seeding:1, progressive_poa:1, put_gap_on_right:, put_gap_at_end:1; // put indel on the left-most side of the alignment: minimap2-like, or right-most: wfa2-like
+    uint8_t sub_aln:1, use_qv:1, disable_seeding:1, progressive_poa:1, put_gap_on_right:1, put_gap_at_end:1; // put indel on the left-most side of the alignment: minimap2-like, or right-most: wfa2-like
     char *incr_fn, *out_pog;
     int align_mode, gap_mode, max_n_cons, cons_algrm; // consensus calling algorithm: 0: partial order graph, 1: majority voting
     double min_freq; // for multiploid data

diff --git a/src/abpoa.h b/src/abpoa.h
@@ -78,7 +78,7 @@ typedef struct {
     // alignment mode
     uint8_t ret_cigar:1, rev_cigar:1, out_msa:1, out_cons:1, out_gfa:1, out_fq:1, use_read_ids:1, amb_strand:1;
     // sub_aln: reads align to subgraph, total read count is based on subgraph coverage, i.e., node.n_span_read, not total input read count
-    uint8_t sub_aln:1, use_qv:1, disable_seeding:1, progressive_poa:1, put_gap_on_right:, put_gap_at_end:1; // put indel on the left-most side of the alignment: minimap2-like, or right-most: wfa2-like
+    uint8_t sub_aln:1, use_qv:1, disable_seeding:1, progressive_poa:1, put_gap_on_right:1, put_gap_at_end:1; // put indel on the left-most side of the alignment: minimap2-like, or right-most: wfa2-like
     char *incr_fn, *out_pog;
     int align_mode, gap_mode, max_n_cons, cons_algrm; // consensus calling algorithm: 0: partial order graph, 1: majority voting
     double min_freq; // for multiploid data