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SHORE API
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SHORE API
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SFF (Standard Flowgram Format) Common Header Section as documented in the GS FLX documentation. More...
Public Attributes | |
| uint32_t | magic |
| char | version [4] |
| uint64_t | index_offset |
| uint32_t | index_length |
| uint32_t | number_of_reads |
| uint16_t | header_length |
| uint16_t | key_length |
| uint16_t | number_of_flows_per_read |
| uint8_t | flowgram_format_code |
| std::string | flow_chars |
| std::string | key_sequence |
SFF (Standard Flowgram Format) Common Header Section as documented in the GS FLX documentation.
| std::string shore::sff_read::commonhead::flow_chars |
The flow_chars should be set to the array of nucleotide bases (‚A‘, ‚C‘, ‚G‘ or ‚T‘) that correspond to the nucleotides used for each flow of each read. (char[number_of_flows_per_read])
| uint8_t shore::sff_read::commonhead::flowgram_format_code |
The flowgram_format_code should be set to the format used to encode each of the flowgram values for each read. Currently, only one flowgram format has been adopted, so this value should be set to 1. The flowgram format code 1 stores each value as a uint16_t, where the floating point flowgram value is encoded as „(int) round(value * 100.0)“, and decoded as „(storedvalue / 100.0)“. In other words, the values are stored as an integer encoding of a limited precision floating point value, keeping 2 places to the right of the decimal point, and capping the values at 655.35.
| uint16_t shore::sff_read::commonhead::header_length |
The header_length field should be the total number of bytes required by this set of header fields, and should be equal to „31 + number_of_flows_per_read + key_length“, rounded up to the next value divisible by 8.
| uint64_t shore::sff_read::commonhead::index_offset |
The index_offset and index_length fields are the offset and length of an optional index of the reads in the SFF file. If no index is included in the file, both fields must be 0.
| uint16_t shore::sff_read::commonhead::key_length |
The key_length field should be set to the length of the key sequence used for these reads.
| std::string shore::sff_read::commonhead::key_sequence |
sequence used for these reads. Note that the key_sequence field is not null-terminated. (char[key_length])
| uint32_t shore::sff_read::commonhead::magic |
The magic_number field value is 0x2E736666, the uint32_t encoding of the string „.sff“.
| uint16_t shore::sff_read::commonhead::number_of_flows_per_read |
The number_of_flows_per_read should be set to the number of flows for each of the reads in the file.
| uint32_t shore::sff_read::commonhead::number_of_reads |
The number_of_reads field should be set to the number of reads stored
| char shore::sff_read::commonhead::version[4] |
The version number is 0001, or the byte array „\0\0\0\1“.
1.8.4 
