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Mathieu Giraud authored Mar 10, 2015 and Vidjil Team committed Mar 10, 2015

http://www.motobit.com/help/scptutl/pa98.htm
Thanks @mikael-s and @duez for pointing out this.

But how can we retrieve the shiftKey inside a d3.js selectAll (scatterPlot.js) ?

- Can select all/no loci
- Can select just one locus

It will be helpful to provide shortcuts for selecting just one.

There is no reason to call the sequence sampler if we already don't have more
sequences than what we would require for the sample.

Before the list was actually stored. Now the list of reads is not stored
anymore.  There are several lists of (some) reads, and for getReads() a single
list is computed from those lists.  We should see if it causes some slow down
but we rarely call getReads() and we don't have anymore to sample sequences.

- Methods for defining parameters of the bins
- Changing the code to fit BinReadStorage methods
- New unit tests to test BinReadStorage

A BinReadStorage is provided which stores reads in bins and
keeps only the reads in the upper bins if there is no space left (to avoid wasting RAM).

This number is set by default to the max_auditioned sequences since we need that many sequences in maximum
(unless we want to see all the sequences).

nb_reads: For consistency reasons the number of reads is stored eveywhere with size_t instead of int

Returns the number of reads for a window.
Previously it could be obtained through getReads().size() but in the future we may not always
store all the reads in memory but just the most abundants.

Mathieu Giraud authored Mar 09, 2015 and Vidjil Team committed Mar 09, 2015

[process] (patient) c'config'
We should even have some utility function in modules/ to do that.

As some decadent OS are case-insensitive for filenames, we should not
have two files whose names only differ in capitalization.

core/windowExtractor.{cpp,h}, vidjil.cpp: option '-X' takes reads at regular intervals from the file

The first reads (now '-x') are sometimes different from the average reads.

Couting the sequences in a Fasta file. Not very efficient, but for debug purposes.

The browser needs to have correct sums in order to display the clones on the grid.
Ideally, we should create pseudo-germlines such as 'TRG!' for these reads.

With this debug option, all unsegmented reads of sufficient length will be kept,
with a fake window being their complete sequence.
These reads can then be seen in the browser.