snpsHts

SnpsHts should be the script dealing with manipulation of the snp fingerprinting from the HTS side.

The script it self is called by MergeResults and consist of a series of functions:

Functions

def GetVcfRecords(vcf_file):

Get the vcf file and return an handle (vcf_reader) as well as an object (vcf_records) representing the variants

def GetSampleName(string): NOT USED

def GetSampleRunDate(string): NOT USED

def GetSampleRunDateAndSampleID(string): NOT USED

def GetSampleID_RunID_Index(string):

def retrieveTaqManfile(string,location): This should be in snpQCreader

			MOVED

And defines a series of variables

Variables

vcf_records list of vcf entries

vcf_reader

sampleID Sample_Diag-excap17-13000217701-KIT-AI50Mbv5

runID 131009_7001448_0224_BC2G61ACXX

index 13000217701

runDate 131009

GF_possibilities list of what ?

TaqManfile

Procedure

1. Get the vcf file into an manageable object via GetVcfRecords.
2. From the vcf filename get the sampleID,runID, index,and runDate via GetSampleID_RunID_Index