Fix an issue of assigning wrong second_min_error. Allow gap beginning in more... (80cf4370) · Commits · github_fork / Chromap

src/chromap.cc

+6 −5

Original line number	Diff line number	Diff line
		@@ -1343,7 +1343,7 @@ void Chromap<MappingRecord>::GenerateBestMappingsForPairedEndReadOnOneDirection(
		}
		best_mappings->emplace_back(i1, i2);
		*min_sum_errors = min_num_errors1 + min_num_errors2;
		*second_min_sum_errors = min_num_errors1 + min_num_errors2 + 1;
		//*second_min_sum_errors = min_num_errors1 + min_num_errors2 + 1;
		(*num_best_mappings)++;
		}
		}
		@@ -2749,8 +2749,8 @@ void Chromap<MappingRecord>::VerifyCandidatesOnOneDirection(Direction candidate_
		// num_errors = -(mapping_end_position - error_threshold_);
		// }
		//} else {
		if (mapping_end_position - error_threshold_ - num_errors >= mapping_length_threshold) {
		num_errors = -(mapping_end_position - error_threshold_ - num_errors);
		if (mapping_end_position - error_threshold_ - num_errors - gap_beginning >= mapping_length_threshold) {
		num_errors = -(mapping_end_position - error_threshold_ - num_errors - gap_beginning);
		} else {
		num_errors = error_threshold_ + 1;
		}
		@@ -3013,7 +3013,7 @@ int Chromap<MappingRecord>::BandedAlignPatternToTextWithDropOff(const char *patt
		*mapping_end_position = band_start_position + 1 + i;
		}
		}
		if (fail_beginning) {
		if (fail_beginning \|\| (read_length > 60 && *mapping_end_position - error_threshold_ - min_num_errors < 30)) {
		mapping_end_position = -mapping_end_position;
		}
		return min_num_errors;
		@@ -3039,6 +3039,7 @@ int Chromap<MappingRecord>::BandedAlignPatternToTextWithDropOffFrom3End(const ch
		int i = 0;
		int fail_beginning = 0; // the alignment failed at the beginning part
		for (; i < read_length; i++) {
		//printf("%c %c %d\n", pattern[read_length - 1 - i], pattern[read_length - 1 - i + error_threshold_], text[read_length - 1 - i]);
		uint8_t pattern_base = SequenceBatch::CharToUint8(pattern[read_length - 1 - i]);
		Peq[pattern_base] = Peq[pattern_base] \| highest_bit_in_band_mask;
		X = Peq[SequenceBatch::CharToUint8(text[read_length - 1 - i])] \| VN;
		@@ -3072,7 +3073,7 @@ int Chromap<MappingRecord>::BandedAlignPatternToTextWithDropOffFrom3End(const ch
		*mapping_end_position = band_start_position + (1 + i);
		}
		}
		if (fail_beginning) {
		if (fail_beginning \|\| (read_length > 60 && *mapping_end_position - error_threshold_ - min_num_errors < 30) ) {
		mapping_end_position = -mapping_end_position;
		}
		return min_num_errors;

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