MACS3.Signal.VariantStat module

Module for SAPPER BAMParser class

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License (see the file COPYING included with the distribution).

@status: experimental @version: $Revision$ @author: Tao Liu @contact: tliu4@buffalo.edu

MACS3.Signal.VariantStat.CalModel_Heter_AS(top1_bq_T, top1_bq_C, top2_bq_T, top2_bq_C, max_allowed_ar=0.99)

Return (lnL, BIC)

kc ki AS_alleleratio

Return type:: tuple

MACS3.Signal.VariantStat.CalModel_Heter_noAS(top1_bq_T, top1_bq_C, top2_bq_T, top2_bq_C)

Return (lnL, BIC)

k_T k_C

Return type:: tuple

MACS3.Signal.VariantStat.CalModel_Homo(top1_bq_T, top1_bq_C, top2_bq_T, top2_bq_C)

Return (lnL, BIC).

Return type:: tuple

MACS3.Signal.VariantStat.GreedyMaxFunctionAS(m, n, tn, me, ne, max_allowed_ar=0.99)

Return lnL, k and alleleratio in tuple.

Note: I only translate Liqing’s C++ code into pyx here. Haven’t done any review.

Return type:: tuple

MACS3.Signal.VariantStat.GreedyMaxFunctionNoAS(m, n, tn, me, ne)

Return lnL, and k in tuple.

Note: I only translate Liqing’s C++ code into pyx here. Haven’t done any review.

Return type:: tuple

MACS3.Signal.VariantStat.bool(*args, **kwargs)

MACS3.Signal.VariantStat.calculate_GQ(lnL1, lnL2, lnL3)

GQ1 = -10*log_{10}((L2+L3)/(L1+L2+L3))

Return type:: typedef

MACS3.Signal.VariantStat.calculate_GQ_heterASsig(lnL1, lnL2)

Return type:: typedef

MACS3.Signal.VariantStat.calculate_ln(m, n, tn, me, ne, r, k, max_allowed_r=0.99): Calculate log likelihood given quality of top1 and top2, the ratio r and the observed k.