Update readme. Use true num_dup as much as possible. (240078dd) · Commits · github_fork / Chromap

chromap.1

+3 −0

Original line number	Diff line number	Diff line
		@@ -253,6 +253,9 @@ Custom chromosome order file for pairs flipping. If not specified, the custom ch
		.BR --barcode-translate \ FILE
		Convert input barcodes to another set of barcodes in the output.
		.TP
		.BR --summary \ FILE
		Summarize the mapping statistics at bulk or barcode level.
		.TP
		.B -v
		Print version number to stdout.

src/chromap.h

+1 −1

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

		#define CHROMAP_VERSION "0.2.4-r467"
		#define CHROMAP_VERSION "0.2.5-r472"

		namespace chromap {

src/chromap_driver.cc

+1 −1

Original line number	Diff line number	Diff line
		@@ -121,7 +121,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		"FILE")("barcode-translate",
		"Convert barcode to the specified sequences during output",
		cxxopts::value<std::string>(), "FILE")
		("summary", "Summarize the mapping metadata at bulk or barcode level",
		("summary", "Summarize the mapping statistics at bulk or barcode level",
		cxxopts::value<std::string>(), "FILE");
		//("PAF", "Output mappings in PAF format (only for test)");
		options.add_options()("v,version", "Print version")("h,help", "Print help");

src/mapping_writer.h

+8 −10

Original line number	Diff line number	Diff line
		@@ -285,17 +285,15 @@ void MappingWriter<MappingRecord>::ProcessAndOutputMappingsInLowMemory(
		++num_mappings_passing_filters;
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_DUP,
		last_mapping.num_dups_ - 1);
		num_last_mapping_dups - 1);
		} else {
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_LOWMAPQ,
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));
		num_last_mapping_dups);
		}
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_MAPPED,
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));
		num_last_mapping_dups);

		if (last_mapping.is_unique_ == 1) {
		++num_uni_mappings;
		@@ -336,17 +334,15 @@ void MappingWriter<MappingRecord>::ProcessAndOutputMappingsInLowMemory(

		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_DUP,
		last_mapping.num_dups_ - 1);
		num_last_mapping_dups - 1);
		} else {
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_LOWMAPQ,
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));
		num_last_mapping_dups);
		}
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_MAPPED,
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));
		num_last_mapping_dups);

		if (last_mapping.is_unique_ == 1) {
		++num_uni_mappings;
		@@ -410,6 +406,8 @@ void MappingWriter<MappingRecord>::OutputMappingsInVector(
		AppendMapping(ri, reference, *it);
		++num_mappings_passing_filters;
		//}
		//it->num_dups_ is capped by 255 here, so the count might be different in the
		// low-mem mode.
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(it->GetBarcode(), SUMMARY_METADATA_DUP,
		it->num_dups_ - 1);

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