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Merge pull request #55 from yhoogstrate/polyN4bit
Poly n4bit
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@@ -25,3 +25,5 @@ xcheck.sh | |
| .ninja* | ||
| test-mount.sh | ||
| *.dict | ||
| *.pyc | ||
| .venv | ||
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| @@ -0,0 +1,92 @@ | ||
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| #include <vector> | ||
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| #include <openssl/md5.h> | ||
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| #include "config.hpp" | ||
| #include "utils.hpp" | ||
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| #include "fastafs.hpp" | ||
| #include "twobit_byte.hpp" | ||
| #include "fourbit_byte.hpp" | ||
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| class fasta_to_fastafs_seq | ||
| { | ||
| public: | ||
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| void add_N(); | ||
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| void add_twobit_ACTG(unsigned char, std::ofstream &);//Adds a T or a U | ||
| void finish_twobit_sequence(std::ofstream &); | ||
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| void add_fourbit_ACTG(unsigned char, std::ofstream &);//Adds a T or a U | ||
| void finish_fourbit_sequence(std::ofstream &); | ||
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| off_t file_offset_in_fasta; // file positions in FASTA file where sequence data blocks starts [ACTG] | ||
| off_t file_offset_in_fastafs; // file positions in FASTAFS file where sequence data blocks starts [2bit/4bit] | ||
| std::string name; | ||
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| uint32_t N;// number of N (unknown) nucleotides (n - N = total 2bit compressed nucleotides) | ||
| uint32_t n_actg;// number of non-N nucleotides (any [ACTGU]) | ||
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| size_t N_bytes_used();// total number of bytes needed to store N's | ||
| size_t twobit_bytes_used();// total number of bytes needed to store xBits | ||
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| bool previous_was_N; | ||
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| // all below are undefined at initialization | ||
| uint32_t padding; | ||
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| // the followin should be member of a conversion struct, because they're not related to the original 2bit format: | ||
| MD5_CTX ctx; | ||
| unsigned char md5_digest[MD5_DIGEST_LENGTH]; | ||
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| std::vector<uint32_t> n_block_starts; | ||
| std::vector<uint32_t> n_block_ends; | ||
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| std::vector<uint32_t> m_block_starts; | ||
| std::vector<uint32_t> m_block_ends; | ||
| bool in_m_block; | ||
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| char current_dict; | ||
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| bool has_T; | ||
| bool has_U; | ||
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| twobit_byte twobit_data; | ||
| fourbit_byte fourbit_data; | ||
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| fasta_to_fastafs_seq(off_t fof_fasta, off_t fof_fastafs, const std::string &name): | ||
| file_offset_in_fasta(fof_fasta), | ||
| file_offset_in_fastafs(fof_fastafs), | ||
| name(name), | ||
| N(0), | ||
| n_actg(0), | ||
| previous_was_N(false), | ||
| in_m_block(false), | ||
| current_dict(DICT_TWOBIT), | ||
| has_T(false), | ||
| has_U(false), | ||
| twobit_data(ENCODE_HASH_TWOBIT_DNA) // not relevant for encoding, only for decoding | ||
| { | ||
| if(name.size() > 255) { | ||
| fprintf(stderr, "[fasta_to_fastafs::init] sequence name truncated to 255 charaters: %s\n", name.c_str()); | ||
| this->name = this->name.substr (0,255); | ||
| } | ||
| MD5_Init(&this->ctx); | ||
| } | ||
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| void flush(); | ||
| }; | ||
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| size_t fasta_to_fastafs(const std::string &, const std::string &, bool auto_recompress_to_fourbit); | ||
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