diff --git a/test/read_bam_file.d b/test/read_bam_file.d index e0b3004..ef13300 100644 --- a/test/read_bam_file.d +++ b/test/read_bam_file.d @@ -346,61 +346,7 @@ CigarOperation[] cigarFromString(string cigar) { assert(equal(sf.reads, bf.reads!withoutOffsets)); } - // stderr.writeln("Testing pileup (high-level aspects)..."); - { - // All of pileup functions should automatically filter out unmapped reads. - // When reads in a range are aligned to different references, - // pileup objects should process only the first one. - bf = new BamReader(fn); // chr1, chr2 - { - auto pileup2 = makePileup(bf.reads); - foreach (column; pileup2) { - foreach (read; column.reads) { - assert(bf.reference_sequences[read.ref_id].name == "chr1"); - assert(read.ref_id == column.ref_id); - assert(!read.is_unmapped); - } - } - } - // However, if pileupColumns is used, columns corresponding to chr1 - // should come first, and after them -- those for chr2 - { - auto columns = pileupColumns(bf.reads); - int current_ref_id = -1; - - // [99 .. 1569] [1 .. 1567] - int[2] expected_columns = [1470, 1567]; - foreach (column; columns) { - int ref_id = column.ref_id; - --expected_columns[ref_id]; - if (ref_id != current_ref_id) { - assert(ref_id > current_ref_id); - switch (ref_id) { - case 0: - assert(column.reads.front.name == "EAS56_57:6:190:289:82"); - assert(column.position == 99); - break; - case 1: - assert(column.reads.front.name == "B7_591:8:4:841:340"); - assert(column.position == 0); - break; - default: - break; - } - - current_ref_id = ref_id; - } - if (!column.reads.empty) { - foreach (read; column.reads) { - assert(read.ref_id == ref_id); - assert(!read.is_unmapped); - } - } - } - assert(expected_columns == [0, 0]); - } - } } }