makeBaseCalls Ab1 file

[dridk]

Some AB1 file doesn't provide base calling from raw trace.
That's mean the following fields are empty and I cannot display the trace : PBAS, PLOC, PCON, DATA.9-14
We need to compute the base balls if they are missing.

@see AB1 specification
http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf

@see R implementation
https://www.bioconductor.org/packages/devel/bioc/vignettes/sangerseqR/inst/doc/sangerseq_walkthrough.pdf

[dridk]

how to compute phred score
https://www.dnastar.com/seqman_pro_help/index.html#!Documents/qualityscorecalculations.htm

[dridk]

https://tools.thermofisher.com/content/sfs/brochures/seq-quantification-app-note.pdf

[dridk]

http://www.insilicase.com/Web/PhredScores.aspx

[dridk]

https://www.ncbi.nlm.nih.gov/pubmed/9521921

[dridk]

http://www.phrap.org/phredphrapconsed.html

[dridk]

3. Algorithms.

   Phred uses simple Fourier methods to examine the four base traces in
   the region surrounding each point in the data set in order to predict
   a series of evenly spaced predicted locations. That is, it determines
   where the peaks would be centered if there were no compressions,
   dropouts, or other factors shifting the peaks from their "true"
   locations.

   Next phred examines each trace to find the centers of the actual, or
   observed, peaks and the areas of these peaks relative to their neighbors.
   The peaks are detected independently along each of the four traces so
   many peaks overlap. A dynamic programming algorithm is used to match
   the observed peaks detected in the second step with the predicted peak
   locations found in the first step.

   Phred evaluates the trace surrounding each called base using four or
   five quality value parameters to quantify the trace quality. It
   uses a quality value lookup table to assign the corresponding quality
   value. The quality value is related to the base call error probability
   by the formula

   QV = - 10 * log_10( P_e )

   where P_e is the probability that the base call is an error.

   Phred uses data from a chemistry parameter file called 'phredpar.dat'
   in order to identify dye primer data. For dye primer data, phred
   identifies loop/stem sequence motifs that tend to result in
   CC and GG merged peak compressions. It reduces the quality values
   of potential merged peaks and splits those peaks that have certain
   trace characteristics indicative of merged CC and GG peaks. In
   addition, the chemistry and dye information are passed to phrap.