Improve HET-model and add RG merging to profiling step

- Change model for HET variants. The model now also considers the distribution of the reads between the reference allele and the variant allele to make overall more accurate predictions.
- Add parameter -q to control the assumed probability of drawing a deletion allele in a HET scenario.
 - Add paramter -f to controll the size of the pseudo counts.
 - Add paramter -mrg to popdel profile to merge all read groups of one sample.
- Fix wrong type of SVLEN INFO field in VCF header.

Add window-wise exclusion of high coverage read groups

Reads from read groups that have high coverage (>= parameter -A or -a) are excluded from calling and genotyping in the respective windows.
Cap GQ at 255.
Fix bug causing wrong assessment of current active coverage after switching to a new ROI/chromosome.

Add GQ and high-coverage loading filter

Add high-coverage filter when reading the profiles. This will reduce workload and false positives in high-coverage regions.
Add genotype quality (GQ) field to VCF output.
Add options (-A, -a) for controlling the high-coverage loading filter.
Update warning and info messages

Fix bug when encountering overlapping deletions.

Fix wrong update of deletion length when a big deletion overlapped a smaller deletion in another sample.
Fix bug in likelihood calculation of regions with extremely high coverage. This fix also slightly reduces the number of false positives called in those regions.
Set default value of -s option to 0.1, as the previous value of 0.75 was much too strict.

Helpful parsing errors

- Make parsing errors during loading of the profiles more verbose so the messages now precisely tell what went wrong in which file.
- Fix non-ciritcal memory leak during parameter calculation of calling step.

Fix bug causing segfault when merging windows

Hotfix for a bug causing segmentation faults when trying to merge a run of filtered windows  followed by a single good window.

New filter and fixes to merging of called windows

Add filter for relative supporting window coverage (default: >=0.5). This improves the precision on real data.
Fix bug that could cause faulty (low) LR values for some variants.
Fix bug that could prevent  filters from being applied.
Add contact info to --help command.

Improve merging of called windows

- Fix bug which could cause an incorrect merge for the last run of coherent calls in a segment.
- Improve variant position estimation.
- Improve allele frequency estimation.
- Improve deletion length estimation.
- Improve likelihood estimation.

Fix bug responsible for crashes after contigs wihout variants

Fix segmentation fault that could occur after processing a contig without any variants.

Fixes and improvements to ROI-handling.

PopDel view now also accepts ROI's consisting only of the contig name (without start and end positions).
PopDel view now also accepts ROI's consisting only of the contig name and the start position (without end position).
Fix bug causing wrong handling of ROI's during calling.
Fix bug causing wrong contig lengths when using ROI's in profile creation.
Fix bug causing duplicate lines in VCF output.
Fix bug causing wrong chromosome names in VCF output.