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Revamping the --somatic_p code in pindel2vcf.cpp#69

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JohnMCMa wants to merge 3 commits intogenome:masterfrom
JohnMCMa:Somatic
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Revamping the --somatic_p code in pindel2vcf.cpp#69
JohnMCMa wants to merge 3 commits intogenome:masterfrom
JohnMCMa:Somatic

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@JohnMCMa JohnMCMa commented Jun 28, 2017

This fixes several bugs involved in the --somatic_p flag in pindel2vcf.

  1. BUGFIX: The somatic p-value is written to the INFO string without a tag. A tag SPV (from the VarScan equivalant) is added to hold this data.
  2. BUGFIX: pindel outputs prior to 0.2.4u don't have ref support count, which may lead to unpredictable results. As a result, the p-values will not be written and a warning will be given to the user if this flag is turned on and the file is of the old format.
  3. BUGFIX: The Fisher's test algorithm implemented used in kfunc.c is copied verbatim to this file but never used. It is now implemented instead of a factorial-based method which is unstable and gives out too much NaN.

This should fix #51 .

JohnMCMa added 3 commits June 28, 2017 09:42
@JohnMCMa
bugfix: Field name for somatic_p
1e34929 
bugfix: Currently when --somatic_p is triggered a p-value is written to
the INFO string without a field name. It is now given a name of SPV from
the equivalant statistic from VarScan
(http://dkoboldt.github.io/varscan/somatic-calling.html)
@JohnMCMa
Un-commenting the option --somatic_p
5f3f1e6
@JohnMCMa
Overhaul of --somatic_p calculation
5fb9690 
* Implementing the algorithm used in htslib (already put in the code but
never called)
* Since files from pindel < 0.2.4u doesn't contain RD, --somatic_p will
be turned off even if the user flags it.
@JohnMCMa JohnMCMa mentioned this pull request Jun 28, 2017
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pindel2vcf error: unknown argument: –so

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