GenomicsDBImport scrambles sample names

[lbergelson]

There was a critical bug in GenomicsDBImport which permuted the sample names of the data in the output GenomicsDB.

This was caused by a mismatch in the sorting of the sample names when files were written to the database, and when the callset.json was written.

The problem only occurred when:

1. the input vcfs (or more likely the sample name mapping file) were not lexicographically sorted
2. 'batchSizeargument was set to something other than0`
3. the number of samples is large enough to be processed in multiple batches.

Each batch is sorted internally by genomicsDB, and the callset.json is sorted separately and globally. Together these produce a mismatch in sample name assignment.

Ex:
Sample name map file:

Sample3	sample3.vcf
Sample1	sample1.vcf
Sample2	sample2.vcf

With batch size 2:

as input:
| Sample3, Sample1 | Sample2 |

as sorted by batch and written:
| Sample1, Sample3 | Sample2 |

as the labels are sorted and recorded:
Sample1, Sample2, Sample3

In this case, Sample2 and Sample3 are mislabelled. This causes call sets genotyped from this database to be mislabelled.

This issue has been fixed in #3667 by sorting the input file globally before passing it to the importer. A tool to fix the labelling of mangled call sets is being added in #3675