Loading chromap.1 +3 −3 Original line number Diff line number Diff line .TH chromap 1 "14 Feb 2022" "chromap-0.1.6 (r309)" "Bioinformatics tools" .TH chromap 1 "22 Feb 2022" "chromap-0.2 (r351)" "Bioinformatics tools" .SH NAME .PP chromap - fast alignment and preprocessing of chromatin profiles Loading Loading @@ -232,7 +232,7 @@ Output file. Output mappings with barcode not in the whitelist. .TP .BR --chr-order \ FILE Customized chromsome order. Custom chromosome order file. If not specified, the order of reference sequences will be used. .TP .BR --BED Output mappings in BED/BEDPE format. Note that only one of the formats should be Loading @@ -248,7 +248,7 @@ Output mappings in SAM format. Output mappings in pairs format (defined by 4DN for HiC data). .TP .BR --pairs-natural-chr-order \ FILE Natural chromosome order for pairs flipping. Custom chromosome order file for pairs flipping. If not specified, the custom chromosome order will be used. .TP .BR --barcode-translate \ FILE Convert input barcodes to another set of barcodes in the output. Loading src/chromap.h +1 −1 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ #include "temp_mapping.h" #include "utils.h" #define CHROMAP_VERSION "0.1.6-r346" #define CHROMAP_VERSION "0.2-r351" namespace chromap { Loading src/chromap_driver.cc +6 −2 Original line number Diff line number Diff line Loading @@ -105,14 +105,18 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { // cxxopts::value<std::string>(), "FILE") ("output-mappings-not-in-whitelist", "Output mappings with barcode not in the whitelist")( "chr-order", "custom chromsome order", cxxopts::value<std::string>(), "chr-order", "Custom chromosome order file. If not specified, the order of " "reference sequences will be used", cxxopts::value<std::string>(), "FILE")("BED", "Output mappings in BED/BEDPE format")( "TagAlign", "Output mappings in TagAlign/PairedTagAlign format")( "SAM", "Output mappings in SAM format")( "pairs", "Output mappings in pairs format (defined by 4DN for HiC data)")( "pairs-natural-chr-order", "natural chromosome order for pairs flipping", "Custom chromosome order file for pairs flipping. If not specified, " "the custom chromosome order will be used", cxxopts::value<std::string>(), "FILE")("barcode-translate", "Convert barcode to the specified sequences during output", Loading Loading
chromap.1 +3 −3 Original line number Diff line number Diff line .TH chromap 1 "14 Feb 2022" "chromap-0.1.6 (r309)" "Bioinformatics tools" .TH chromap 1 "22 Feb 2022" "chromap-0.2 (r351)" "Bioinformatics tools" .SH NAME .PP chromap - fast alignment and preprocessing of chromatin profiles Loading Loading @@ -232,7 +232,7 @@ Output file. Output mappings with barcode not in the whitelist. .TP .BR --chr-order \ FILE Customized chromsome order. Custom chromosome order file. If not specified, the order of reference sequences will be used. .TP .BR --BED Output mappings in BED/BEDPE format. Note that only one of the formats should be Loading @@ -248,7 +248,7 @@ Output mappings in SAM format. Output mappings in pairs format (defined by 4DN for HiC data). .TP .BR --pairs-natural-chr-order \ FILE Natural chromosome order for pairs flipping. Custom chromosome order file for pairs flipping. If not specified, the custom chromosome order will be used. .TP .BR --barcode-translate \ FILE Convert input barcodes to another set of barcodes in the output. Loading
src/chromap.h +1 −1 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ #include "temp_mapping.h" #include "utils.h" #define CHROMAP_VERSION "0.1.6-r346" #define CHROMAP_VERSION "0.2-r351" namespace chromap { Loading
src/chromap_driver.cc +6 −2 Original line number Diff line number Diff line Loading @@ -105,14 +105,18 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { // cxxopts::value<std::string>(), "FILE") ("output-mappings-not-in-whitelist", "Output mappings with barcode not in the whitelist")( "chr-order", "custom chromsome order", cxxopts::value<std::string>(), "chr-order", "Custom chromosome order file. If not specified, the order of " "reference sequences will be used", cxxopts::value<std::string>(), "FILE")("BED", "Output mappings in BED/BEDPE format")( "TagAlign", "Output mappings in TagAlign/PairedTagAlign format")( "SAM", "Output mappings in SAM format")( "pairs", "Output mappings in pairs format (defined by 4DN for HiC data)")( "pairs-natural-chr-order", "natural chromosome order for pairs flipping", "Custom chromosome order file for pairs flipping. If not specified, " "the custom chromosome order will be used", cxxopts::value<std::string>(), "FILE")("barcode-translate", "Convert barcode to the specified sequences during output", Loading
