Fix a bug in summary the alignment stats when outputing SAM format (4af36173) · Commits · github_fork / Chromap

src/chromap.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -1119,6 +1119,8 @@ void Chromap::MapPairedEndReads() {
		// }
		//}
		}
		if (mapping_parameters_.mapping_output_format == MAPPINGFORMAT_SAM)
		mapping_writer.AdjustSummaryPairedEndOverCount() ;
		mapping_writer.OutputSummaryMetadata();

		reference.FinalizeLoading();

+12 −0

Original line number	Diff line number	Diff line
		@@ -70,6 +70,7 @@ class MappingWriter {

		void OutputSummaryMetadata();
		void UpdateSummaryMetadata(uint64_t barcode, int type, int change);
		void AdjustSummaryPairedEndOverCount();

		protected:
		void AppendMapping(uint32_t rid, const SequenceBatch &reference,
		@@ -438,8 +439,10 @@ void MappingWriter<MappingRecord>::OutputMappings(
		template <typename MappingRecord>
		void MappingWriter<MappingRecord>::OutputSummaryMetadata() {
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		{
		summary_metadata_.Output(mapping_parameters_.summary_metadata_file_path.c_str());
		}
		}

		template <typename MappingRecord>
		void MappingWriter<MappingRecord>::UpdateSummaryMetadata(uint64_t barcode, int type, int change)
		@@ -448,6 +451,15 @@ template <typename MappingRecord>
		summary_metadata_.UpdateCount(barcode, type, change);
		}

		template <typename MappingRecord>
		void MappingWriter<MappingRecord>::AdjustSummaryPairedEndOverCount()
		{
		if (!mapping_parameters_.summary_metadata_file_path.empty()
		&& mapping_parameters_.mapping_output_format == MAPPINGFORMAT_SAM)
		summary_metadata_.AdjustPairedEndOverCount() ;
		}


		// Specialization for BED format.
		template <>
		void MappingWriter<MappingWithBarcode>::OutputHeader(

+11 −0

Original line number	Diff line number	Diff line
		@@ -75,6 +75,17 @@ class SummaryMetadata {
		barcode_length_ = l;
		}

		// In SAM format for paired-end data, some count will be counted twice
		void AdjustPairedEndOverCount() {
		khiter_t k;
		for (k = kh_begin(barcode_metadata_); k != kh_end(barcode_metadata_); ++k)
		if (kh_exist(barcode_metadata_, k)) {
		kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_DUP] /= 2 ;
		kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_LOWMAPQ] /= 2 ;
		kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_MAPPED] /= 2 ;
		}
		}

		private:
		khash_t(k64_barcode_metadata) *barcode_metadata_;
		int barcode_length_;