Make min. coverage settable.
Rework genotyping script.

1. Cleanup and document (partial)
2. Split large intervals (>1kb) into fragments, in order to ensure
   that memory usage stays reasonable for e.g. whole chromosomes.
3. Allow use of unfiltered VCFs (FILTERED == .)
Stricter limits for prefix/target names.

1. Only allow alpha-numerical, and ., -, and _.
2. Require that names for target fields are at least 2 chars;
   this is needed to prevent implicit conversion of tag-types
   by pysam from string to char, which causes failure downstream.
3. Disallow various chars in prefix paths, which may cause
   problems for e.g. Bowtie2.
Fix rare case of spurious insertions.

This fixes a rare case where spurious insertions could be added to
sequences, if two conditions were met: Firstly, the insertion had
to start before the sequence, and secondly the resulting negative
position (indel.pos - start) had to extend past the 5' padding.

This was exposed due to the removal of 5' padding.