V-Phaser 2 p-value computation is unstable

[Irwin Jungreis]

When V-Phaser 2 is tested on the sample file with which it is distributed, 4528.454.indelRealigned.bam, some of the p-values in the resulting .txt files vary from run to run. Only the .txt files vary; the other files are the same. Only the "Strd_bias_pval" field varies. After running it 10 times, 5 of them produced the same p-values, 3 of the remaining ones produced the same p-values as each other, and the p-values in the remaining 2 runs were different from each other and from the other runs.

Here's a sample diff:

> diff output1/V4528_assembly.var.raw.txt output2
32c32
< 2872    A    G    0.2215    snp    0.7186    A:1:5    G:436:393
---
> 2872    A    G    0.3361    snp    0.7186    A:1:5    G:436:393
41c41
< 3260    C    A    0.4104    snp    0.7018    A:506:343    C:1:5
---
> 3260    C    A    0.5249    snp    0.7018    A:506:343    C:1:5
57c57
< 4236    G    A    0.6867    snp    0.5566    A:534:538    G:2:4
---
> 4236    G    A    0.6939    snp    0.5566    A:534:538    G:2:4
134c134
< 8191    A    T    0.6692    snp    1.354    A:1:5    T:296:141
---
> 8191    A    T    0.7388    snp    1.354    A:1:5    T:296:141

[Irwin Jungreis]

I also note that on other runs some of the differing p-values are interesting. For example, -3.105e+231.