Update SAUtils for Cosmic

[heseber]

Current COSMIC releases have a slightly modified format of the TSV files. Some column headers have changed (e.g., Mutation ID -> GENOMIC_MUTATION_ID, and a new Tier column was added.

Counts for CancerType and CancerSite were based on study identifiers, not on tumor identifiers. This does not really make sense, because we want to know the number of tumors per cancerType and cancerSite, not the number of studies (a study can have many different tumors of the same type and site). Furthermore, the study id column is often empty if a PubMed id is specified instead.

This pull request updates the SAUtils for Cosmic to make it work with current Cosmic releases and also changes the counts to refer to tumors instead of studies. This is only for short variants, not for structural variants and fusions.

Here is an example output (just the "cosmic" section, and after pretty-printing with jq, of course):

"cosmic": [
            {
              "id": "COSV55892885",
              "refAllele": "A",
              "altAllele": "T",
              "gene": "PIK3CA",
              "sampleCount": 5,
              "cancerTypesAndCounts": [
                {
                  "cancerType": "carcinoma",
                  "count": 5
                }
              ],
              "cancerSitesAndCounts": [
                {
                  "cancerSite": "ovary",
                  "count": 3
                },
                {
                  "cancerSite": "large intestine",
                  "count": 2
                }
              ],
              "tiersAndCounts": [
                {
                  "tier": "1",
                  "count": 5
                }
              ]
            }
]