diff options
Diffstat (limited to 'c/importgfa.c')
| -rw-r--r-- | c/importgfa.c | 29 |
1 files changed, 21 insertions, 8 deletions
diff --git a/c/importgfa.c b/c/importgfa.c index 43cc948..d2edb70 100644 --- a/c/importgfa.c +++ b/c/importgfa.c @@ -54,6 +54,11 @@ static uint8_t orientation2int (char c) return c == '+' ? 0 : 1; } +static char invert_orientation (char c) +{ + return c == '+' ? '-' : '+'; +} + static void pass1_handle_s_line (char *line, str_int_map *segment_id_table, duckdb_appender *appender) { static int segment_id = 0; @@ -122,14 +127,22 @@ static void process_l_lines (char **lines, size_t line_count, str_int_map *segme char *original_line = lines[line_index]; // Split L line and write results into data chunk. strsep(&lines[line_index], "\t"); - from_segment_data[chunk_index] - = hashtable_get(segment_id_table, strsep(&lines[line_index], "\t")); - from_orientation_data[chunk_index] - = orientation2int(*strsep(&lines[line_index], "\t")); - to_segment_data[chunk_index] - = hashtable_get(segment_id_table, strsep(&lines[line_index], "\t")); - to_orientation_data[chunk_index] - = orientation2int(*strsep(&lines[line_index], "\t\n")); + int from_segment = hashtable_get(segment_id_table, strsep(&lines[line_index], "\t")); + char from_orientation = *strsep(&lines[line_index], "\t"); + int to_segment = hashtable_get(segment_id_table, strsep(&lines[line_index], "\t")); + char to_orientation = *strsep(&lines[line_index], "\t\n"); + // Canonicalize L line by ensuring from_segment <= to_segment. + if (from_segment <= to_segment) { + from_segment_data[chunk_index] = from_segment; + from_orientation_data[chunk_index] = orientation2int(from_orientation); + to_segment_data[chunk_index] = to_segment; + to_orientation_data[chunk_index] = orientation2int(to_orientation); + } else { + from_segment_data[chunk_index] = to_segment; + from_orientation_data[chunk_index] = orientation2int(invert_orientation(to_orientation)); + to_segment_data[chunk_index] = from_segment; + to_orientation_data[chunk_index] = orientation2int(invert_orientation(from_orientation)); + } free(original_line); } // Write chunk to database. |