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SHORE API
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SHORE API
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SFF (Standard Flowgram Format) Read Header Section as documented in the GS FLX documentation. More...
Public Attributes | |
| uint16_t | read_header_length |
| uint16_t | name_length |
| uint32_t | number_of_bases |
| uint16_t | clip_qual_left |
| uint16_t | clip_qual_right |
| uint16_t | clip_adapter_left |
| uint16_t | clip_adapter_right |
| std::string | name |
SFF (Standard Flowgram Format) Read Header Section as documented in the GS FLX documentation.
| uint16_t shore::sff_read::readhead::clip_qual_left |
The clip_qual_left and clip_adapter_left fields should be set to the position of the first base after the clipping point, for quality and/or an adapter sequence, at the beginning of the read. If only a combined clipping position is computed, it should be stored in clip_qual_left.
The clip_qual_right and clip_adapter_right fields should be set to the position of the last base before the clipping point, for quality and/or an adapter sequence, at the end of the read. If only a combined clipping position is computed, it should be stored in clip_qual_right.
Note that the position values use 1-based indexing, so the first base is at position 1. If a clipping value is not computed, the field should be set to 0.
Thus, the first base of the insert is: max(1, max(clip_qual_left, clip_adapter_left))
...and the last base of the insert is: min( (clip_qual_right == 0 ? number_of_bases : clip_qual_right), (clip_adapter_right == 0 ? number_of_bases : clip_adapter_right) )
| std::string shore::sff_read::readhead::name |
The name field should be set to the string of the read‘s accession or name. Note that the name field is not null-terminated. (char[name_length])
| uint16_t shore::sff_read::readhead::name_length |
The name_length field should be set to the length of the read‘s acces- sion or name.
| uint32_t shore::sff_read::readhead::number_of_bases |
The number_of_bases should be set to the number of bases called for this read.
| uint16_t shore::sff_read::readhead::read_header_length |
The read_header_length should be set to the length of the read header for this read, and should be equal to „16 + name_length“ rounded up to the next value divisible by 8.
1.8.4 
