Fix a bug for hashing 32 bp sequences. (7f283b6f) · Commits · github_fork / Chromap

src/barcode_translator.h

+3 −3

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@
		#include <vector>

		#include "khash.h"
		#include "sequence_batch.h"
		#include "utils.h"

		namespace chromap {

		@@ -108,8 +108,8 @@ class BarcodeTranslator {
		to = line.substr(0, i);
		// from = line.substr(i + 1, len - i - 1);
		from_bc_length_ = len - i - 1;
		uint64_t from_seed = SequenceBatch::GenerateSeedFromSequence(
		line.c_str(), len, i + 1, from_bc_length_);
		uint64_t from_seed =
		GenerateSeedFromSequence(line.c_str(), len, i + 1, from_bc_length_);

		int khash_return_code;
		khiter_t barcode_translate_table_iter = kh_put(

+1 −1

Original line number	Diff line number	Diff line
		@@ -357,7 +357,7 @@ void Chromap::LoadBarcodeWhitelist() {
		// //first_line = false;
		//}
		// assert(kmer.length() == (size_t)kmer_size_);
		uint64_t barcode_key = SequenceBatch::GenerateSeedFromSequence(
		uint64_t barcode_key = GenerateSeedFromSequence(
		barcode.data(), barcode_length, 0, barcode_length);
		// PoreModelParameters &pore_model_parameters =
		// pore_models_[kmer_hash_value]; barcode_whitelist_file_line_string_stream

+1 −1

+3 −37

Original line number	Diff line number	Diff line
		@@ -164,43 +164,9 @@ class SequenceBatch {
		uint32_t start_position,
		uint32_t seed_length) const {
		const char *sequence = GetSequenceAt(sequence_index);
		uint32_t sequence_length = GetSequenceLengthAt(sequence_index);
		uint64_t mask = (((uint64_t)1) << (2 * seed_length)) - 1;
		uint64_t seed = 0;
		for (uint32_t i = 0; i < seed_length; ++i) {
		if (start_position + i < sequence_length) {
		uint8_t current_base = CharToUint8(sequence[i + start_position]);
		if (current_base < 4) { // not an ambiguous base
		seed = ((seed << 2) \| current_base) & mask; // forward k-mer
		} else {
		seed = (seed << 2) & mask; // N->A
		}
		} else {
		seed = (seed << 2) & mask; // Pad A
		}
		}
		return seed;
		}

		inline static uint64_t GenerateSeedFromSequence(const char *sequence,
		uint32_t sequence_length,
		uint32_t start_position,
		uint32_t seed_length) {
		uint64_t mask = (((uint64_t)1) << (2 * seed_length)) - 1;
		uint64_t seed = 0;
		for (uint32_t i = 0; i < seed_length; ++i) {
		if (start_position + i < sequence_length) {
		uint8_t current_base = CharToUint8(sequence[i + start_position]);
		if (current_base < 4) { // not an ambiguous base
		seed = ((seed << 2) \| current_base) & mask; // forward k-mer
		} else {
		seed = (seed << 2) & mask; // N->A
		}
		} else {
		seed = (seed << 2) & mask; // Pad A
		}
		}
		return seed;
		const uint32_t sequence_length = GetSequenceLengthAt(sequence_index);
		return GenerateSeedFromSequence(sequence, sequence_length, start_position,
		seed_length);
		}

		inline void ReorderSequences(const std::vector<int> &rid_rank) {

+21 −0

Original line number	Diff line number	Diff line
		@@ -109,6 +109,27 @@ inline static char Uint8ToChar(const uint8_t i) {
		return uint8_to_char_table_[i];
		}

		// Make sure the length is not greater than 32 before calling this function.
		inline static uint64_t GenerateSeedFromSequence(const char *sequence,
		uint32_t sequence_length,
		uint32_t start_position,
		uint32_t seed_length) {
		uint64_t seed = 0;
		for (uint32_t i = 0; i < seed_length; ++i) {
		if (start_position + i < sequence_length) {
		uint8_t current_base = CharToUint8(sequence[i + start_position]);
		if (current_base < 4) { // not an ambiguous base
		seed = (seed << 2) \| current_base; // forward k-mer
		} else {
		seed = seed << 2; // N->A
		}
		} else {
		seed = seed << 2; // Pad A
		}
		}
		return seed;
		}

		} // namespace chromap

		#endif // UTILS_H_