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query_info.txt
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Queries:
-------------------------------------------------------------------------------
1. Function: query_sample_from_ref
Given: starting position (pos_x), ending position (pos_y), patient's id (sample_id),
Return: the sequence of the patient's genome from pos_x to pos_y (exclusively) in the reference coordinate.
Implementation: done.
Manual test: done.
Correctness test: TBD.
-------------------------------------------------------------------------------
2. Function: query_sample_from_sample
Given: starting position (pos_x), ending position (pos_y), patient's id (sample_id),
Return: the sequence of patient's genome from pos_x to pos_y (exclusively) in the reference coordinate.
Implementation: done.
Manual test: done.
Correctness test: done on small sample without consecutive mutations.
-------------------------------------------------------------------------------
3. Function: closest_var
Given: a position (pos),
Return: the variant in the reference that is closest to the pos.
Implementation: TBD.
Manual test: TBD.
Correctness test: TBD.
-------------------------------------------------------------------------------
4. Function: get_sample_var_in_ref
Given: starting position (pos_x), ending position (pos_y), patient's id (sample_id),
Return: the variants in the patient's genome from pos_x to pos_y (exclusively) in the reference's coordinate.
Implementation: done.
Manual test: done.
Correctness test: TBD.
-------------------------------------------------------------------------------
5. Function: get_sample_var_in_sample
Given: starting position (pos_x), ending position (pos_y), patient's id (sample_id),
Return: the variants in the patient's genome from pos_x to pos_y (exclusively) in the patient's coordinate.
Implementation: done.
Manual test: done.
Correctness test: TBD.
-------------------------------------------------------------------------------
6. Function: get_var_in_ref
Given: starting position (pos_x), ending position (pos_y),
Return: all the variants from pos_x to pos_y (exclusively) in the reference's coordinate.
Implementation: done.
Manual test: done.
Correctness test: TBD.
-------------------------------------------------------------------------------
7. Function: samples_has_var
Given: a variant (pos in the reference coordinate, ref sequence, alt sequence),
Return: all the samples that have such variant.
Implementation: done.
Manual test: done.
Correctness test: TBD.