#include <genesis/population/functions/functions.hpp>
Definition at line 50 of file population/functions/functions.hpp.
Public Attributes | |
bool | is_biallelic = false |
Is the Sample biallelic? More... | |
bool | is_covered = false |
Is the Sample covered by enough reads/nucleotides? More... | |
bool | is_ignored = false |
Is the Sample ignored due to high deletions count? More... | |
bool | is_snp = false |
Does the Sample have two or more alleles? More... | |
bool is_biallelic = false |
Is the Sample biallelic?
This is closely related to Sample::is_snp, but only true
iff the number of nucleotide counts above zero is exactly two - that is, if there are only reads of two of A
, C
, G
, T
in the sample.
This value is also false
if the amount of deletions (Sample::d_count) is too high (using min_count() as the inclusive threshold), unless tolerate_deletions() is true
.
Definition at line 89 of file population/functions/functions.hpp.
bool is_covered = false |
Is the Sample covered by enough reads/nucleotides?
This value is set to true
iff the total Sample::nucleotide_count (sum of Sample::a_count, Sample::c_count, Sample::g_count, and Sample::t_count after testing that they are at least min_count()) is in between the min_coverage() and max_coverage() values (inclusive), and iff the amount of deletions (Sample::d_count) is not higher than min_count() as well (unless, tolerate_deletions() is also set to true
).
That was a mouthful. Basically, a Sample is covered, if the sum of A
, C
, G
, T
is in between min_coverage() and max_coverage(), and (unless we tolerate that) the amount of deletions is not too high.
Definition at line 65 of file population/functions/functions.hpp.
bool is_ignored = false |
Is the Sample ignored due to high deletions count?
This value is only set to true
iff the Sample is well covered (as determined by Sample::is_covered), but also has a high amount of deletions (at least min_count() many), and if not also tolerate_deletions() is true
.
It is hence an indicator that there are too many deletions in the sample (if we decide not to tolerate them).
Definition at line 101 of file population/functions/functions.hpp.
bool is_snp = false |
Does the Sample have two or more alleles?
That is the case if at least two of the A
, C
, G
, T
counts (Sample::a_count, Sample::c_count, Sample::g_count, and Sample::t_count ) are above zero, after testing that they are at least min_count().
This value is also false
if the amount of deletions (Sample::d_count) is too high (using min_count() as the inclusive threshold), unless tolerate_deletions() is true
.
Definition at line 77 of file population/functions/functions.hpp.