989
89%
master: %

Ran 25 Sep 2014 03:48PM UTC

Jobs 1

Files 83

Run time 36s

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Build # 989

Build Type

push

travis-ci

Committed by

MauricioCarneiro

Commit Message

Genotype: add convenience functions: snp, indel...

This is a tricky request from Louis which I anticipate to be a big hit
with the compbios. Everyone wants to query directly at the genotype what
kind of event it is. The problem is that doing so is expensive. One
should always strive to batch this kind of computation across all
samples using functionality like select_if or simple for_each loops.

However sometimes you want to just query one or two of these conditions
and it is nice to have such convenience functions. I strived here to
achieve as much performance as possible without increasing the state of
the Genotype object. To avoid string comparisons, all member functions
rely on an AlleleMask that pre-computes the string differences in the
alt/ref fields only once. All functions operate on key comparisons only.

Still, if you are going to use this for multiple comparisons such as:

```c++
if (genotype.insertion() || genotype.snp() && genotype.simple())
  do_something(genotype);
```

You will most likely be better off writing your own for loop instead of
paying for 3 passes on the data. But for quick queries in data with few
alleles (like diploids) this should be fine.

closes #204

Run Details

1367 of 1530 relevant lines covered (89.35%)

861.77 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	989.1	25 Sep 2014 03:48PM UTC	83	89.35	Travis Job 989.1

Source Files on build 989

Coverage	∆	File	Lines	Relevant	Covered	Missed	Hits/Line

broadinstitute / gamgee / 989
89%
master: %

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