Module libprosic::model::sample [−] [src]

Structs

InsertSize	Expected insert size in terms of mean and standard deviation. This should be estimated from unsorted(!) bam files to avoid positional biases.
Observation	An observation for or against a variant.
RecordBuffer	Ringbuffer of BAM records. This data structure ensures that no bam record is read twice while extracting observations for given variants.
Sample	A sequenced sample, e.g., a tumor or a normal sample.

Evidence
RecordBufferError

adjust_mapq	We assume that the mapping quality of split alignments provided by the aligner is conditional on being no artifact. Artifact alignments can be caused by aligning short ends as splits due to e.g. repeats. We can calculate the probability of having no artifact by investigating if there is at least one full fragment supporting the alternative allele (via enlarged or reduced insert size). Then, the final mapping quality can be obtained by multiplying this probability.
isize_density	Continuous normal density (obsolete).
isize_density_louis	Manual normal density (obsolete, we can use GSL (see above)).
isize_mixture_density_louis
isize_pmf	as shown in http://www.milefoot.com/math/stat/pdfc-normaldisc.htm
prob_mapping	Convert MAPQ (from read mapper) to LogProb for the event that the read maps correctly.