GENIE Subset Script Updates

[rmadupuri]

upload of genie study data (10.x series) - post-processing can be automated for data corrections

also involves fix to angelica's python script referenced here:
subset script for genie outputs incomplete patient clinical data#258

@ao508 may give pointer to script location

PR: knowledgesystems/cmo-pipelines#819

Fixes made:

1. CNA Gene Merge Tool: CNA Gene Merge Tool cmo-pipelines#653
   Script that will take a CNA file and perform the following gene merges:
   CDKN2Ap16/14 -> CDKN2A
   MLLs -> KMTs (MLL, MLL2, MLL3 and MLL4 -> KMT2A KMT2B KMT2C KMT2D)
   FAM123B -> AMER1
   MYCL1 -> MYCL

2. Remove duplicate variants from MAF
   Script to remove duplicate maf records based on the 8 key columns (Entrez_Gene_Id, Chromosome, Start_Position, End_Position, Variant_Classification, Tumor_Seq_Allele2, Tumor_Sample_Barcode, HGVSp_Short)
   Calculates VAF for each record and picks the record with high VAF
   Formula for VAF = t_alt_count / (t_ref_count + t_alt_count)

3. Missing patient ids in patient file GENIE submission process - patient ids with no attributes are missing in patient file. cmo-pipelines#654
   Patients that have no attributes only appear in the sample clinical data file.

4. Vital status location change GENIE submission process - vital status location change cmo-pipelines#657
   Patient vital status attributes were moved from the patient file into vital_status.txt. Since they GENIE has reversed that decision and now wants vital status information back in the patient clinical file.

5. Change value for clinical attributes with no value GENIE submission process - change value for clinical attributes with no value. cmo-pipelines#656
   AGE_AT_SEQ_REPORT, ONCOTREE_CODE, BIRTH_YEAR, YEAR_DEATH, YEAR_CONTACT, INT_CONTACT, INT_DOD cannot be NA or blank. All attribute values should be "Unknown" when the patient/attribute or sample/attribute pair is missing a value.
   Also, for attributes that take on NAACR values, like SEX, PRIMARY_RACE, SECONDARY_RACE, TERTIARY_RACE, ETHNICITY, they should take on the NAACR value for NA - (SEX = 9, RACE = 99, ETHNICITY = 9)

6. Gene panel names missing prefix in clinical file GENIE submission process - gene panel names missing prefix in clinical file. cmo-pipelines#655
   In the "Sequence Assay ID" column of the data_clinical_sample.txt file, IMPACT panel names should be prefixed with an "MSK-".