Add the row that summarize the number of fragments that can not be barcode corrected (4673c364) · Commits · github_fork / Chromap

src/chromap.h

+12 −1

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.2.7-r492"
		#define CHROMAP_VERSION "0.2.7-r493"

		namespace chromap {

		@@ -441,12 +441,18 @@ void Chromap::MapSingleEndReads() {
		mapping_writer.UpdateSummaryMetadata(0, SUMMARY_METADATA_TOTAL,
		num_loaded_reads) ;
		else {
		uint32_t nonwhitelist_count = 0;
		for (uint32_t read_index = 0; read_index < num_loaded_reads; ++read_index)
		if (read_map_summary[read_index] & 1) {
		mapping_writer.UpdateSummaryMetadata(
		barcode_batch.GenerateSeedFromSequenceAt(read_index, 0, barcode_length_),
		SUMMARY_METADATA_TOTAL, 1);
		} else {
		++nonwhitelist_count;
		}

		mapping_writer.UpdateSpeicalCategorySummaryMetadata(/nonwhitelist/0,
		SUMMARY_METADATA_TOTAL, nonwhitelist_count);
		}

		// By default, set the lowest bit to 1 (whether the barcode is in the whitelist)
		@@ -1015,12 +1021,17 @@ void Chromap::MapPairedEndReads() {
		mapping_writer.UpdateSummaryMetadata(0, SUMMARY_METADATA_TOTAL,
		num_loaded_pairs) ;
		else {
		uint32_t nonwhitelist_count = 0 ;
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs; ++pair_index)
		if (read_map_summary[pair_index] & 1) {
		mapping_writer.UpdateSummaryMetadata(
		barcode_batch.GenerateSeedFromSequenceAt(pair_index, 0, barcode_length_),
		SUMMARY_METADATA_TOTAL, 1);
		} else {
		++nonwhitelist_count ;
		}
		mapping_writer.UpdateSpeicalCategorySummaryMetadata(/nonwhitelist/0,
		SUMMARY_METADATA_TOTAL, nonwhitelist_count);
		}

		memset(read_map_summary, 1, sizeof(read_map_summary)read_batch_size_);

src/mapping_writer.h

+14 −5

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 UpdateSpeicalCategorySummaryMetadata(int category, int type, int change);
		void AdjustSummaryPairedEndOverCount();

		protected:
		@@ -446,20 +447,28 @@ 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());
		summary_metadata_.Output(mapping_parameters_.summary_metadata_file_path.c_str(),
		!mapping_parameters_.barcode_whitelist_file_path.empty() && !mapping_parameters_.output_mappings_not_in_whitelist);
		}
		}

		template <typename MappingRecord>
		void MappingWriter<MappingRecord>::UpdateSummaryMetadata(uint64_t barcode, int type, int change)
		{
		void MappingWriter<MappingRecord>::UpdateSummaryMetadata(uint64_t barcode, int type, int change) {
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(barcode, type, change);
		}

		// category: 0: non-whitelist barcode
		template <typename MappingRecord>
		void MappingWriter<MappingRecord>::AdjustSummaryPairedEndOverCount()
		{
		void MappingWriter<MappingRecord>::UpdateSpeicalCategorySummaryMetadata(int category, int type, int change) {
		if (!mapping_parameters_.summary_metadata_file_path.empty()) {
		if (category == 0)
		summary_metadata_.UpdateNonWhitelistCount(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() ;

src/summary_metadata.h

+24 −11

Original line number	Diff line number	Diff line
		@@ -41,22 +41,30 @@ class SummaryMetadata {
		kh_destroy(k64_barcode_metadata, barcode_metadata_);
		}

		void Output(const char *filename) {
		void OutputCounts(const char barcode, const int counts, FILE *fp)
		{
		fprintf(fp, "%s", barcode) ;
		int i ;
		for (i = 0; i < SUMMARY_METADATA_FIELDS; ++i) {
		if (i != SUMMARY_METADATA_MAPPED)
		fprintf(fp, ",%d", counts[i]);
		else // The output in the summary is for unmapped reads
		fprintf(fp, ",%d", counts[SUMMARY_METADATA_TOTAL] - counts[SUMMARY_METADATA_MAPPED]) ;
		}
		fprintf(fp, "\n");
		}

		void Output(const char *filename, bool has_white_list) {
		FILE *fp = fopen(filename, "w");
		fprintf(fp, "barcode,total,duplicate,unmapped,lowmapq\n");
		khiter_t k;
		for (k = kh_begin(barcode_metadata_); k != kh_end(barcode_metadata_); ++k)
		if (kh_exist(barcode_metadata_, k)) {
		fprintf(fp, "%s", Seed2Sequence(kh_key(barcode_metadata_, k), barcode_length_).c_str());
		int i;
		for (i = 0; i < SUMMARY_METADATA_FIELDS; ++i) {
		if (i != SUMMARY_METADATA_MAPPED)
		fprintf(fp, ",%d", kh_value(barcode_metadata_, k).counts[i]);
		else
		fprintf(fp, ",%d", kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_TOTAL]
		- kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_MAPPED]);
		OutputCounts(Seed2Sequence(kh_key(barcode_metadata_, k), barcode_length_).c_str(),
		kh_value(barcode_metadata_, k).counts, fp) ;
		}
		fprintf(fp, "\n");
		if (has_white_list) {
		OutputCounts("non-whitelist", nonwhitelist_summary_.counts, fp) ;
		}
		fclose(fp);
		}
		@@ -71,6 +79,10 @@ class SummaryMetadata {
		kh_value(barcode_metadata_, barcode_metadata_iter).counts[type] += change;
		}

		void UpdateNonWhitelistCount(int type, int change) {
		nonwhitelist_summary_.counts[type] += change;
		}

		void SetBarcodeLength(int l) {
		barcode_length_ = l;
		}
		@@ -88,6 +100,7 @@ class SummaryMetadata {

		private:
		khash_t(k64_barcode_metadata) *barcode_metadata_;
		struct _barcodeSummaryMetadata nonwhitelist_summary_; // summarize the fragments with no barcode information
		int barcode_length_;

		std::string Seed2Sequence(uint64_t seed, uint32_t seed_length) const {

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