Svtools

* Simplify download from GCS so fewer permissions are required
* `create_coordinates` script can open `.gz` files directly

* Bugfix for cases where start and end breakpoints get reversed (https://github.com/brentp/smoove/issues/56)
* Handle INS variants in `lmerge`
* Allow input file paths on GCS (with `gs://` prefixes). These files will be transparently downloaded. The user can optionally specify the temp directory to download to with `--tempdir`
* New svtyper with a bugfix (v0.7.1)

Major changes
- SVTyper has been updated to 0.7.0 which brings in improvements to genotyping quality, duplication sensitivity and speed improvements (courtesy of brentp) for CRAM files.
- Support for 8-column VCFs.
- Introduction of a protocol for tiered-merging for very large cohorts via enhancements to `svtools lmerge`. Thanks to abelhj.
- Multiple fixes to the classifier including manual specification of sex chromosomes which fixed a key bug when chromosomes were prefixed with a 'chr'.
- Fixes to `svtools varlookup` for bugs in parsing the INFO field.
- Fixed a major bug in `svtools prune` which occasionally resulted in incorrect results.
- Set the copynumber for the entire sample to -1 if CNVnator is unable to genotype the sample correctly. Previously `svtools copynumber` would die upon encountering a -1 which resulted in truncated files.
- Fixed a parsing bug in `svtools vcftobedpe` for BNDs on chromosomes containing a `:` in their name.

Minor changes
- Multiple documentation improvements.
- More helpful error handling in a number of situations.
- Better support for manta VCFs.

Major Changes
- svtyper has been updated to v0.1.2 which fixes an issue with estimating library insert sizes from CRAM files.

Major Changes
- svtyper has been updated to v0.1.1 which fixes an issue where `DUP` and `INV` variants were being genotyped incorrectly.

Major Changes
- More unified and consistent user interface, please check tool options as they may have changed.
- Moves to using v0.1.0 of SVTyper for `svtools genotype`. The new version is faster, uses less memory, doesn't require special tags, doesn't require a splitters file and **is more accurate**. Go cc2qe!
- Major bug fix where format field definition could shuffle independent of the data fields. This only happened where the header order was different than the line's order when running `svtools afreq`.
- Usability improvements to `svtools lsort`. It can now take in a list of files (and they can be gzipped) and will skip sites where all samples are homozygous ref by default.
- Multiple improvements to`svtools prune`. Fixes a bug where the variant we intended to prune was actually retained. `SNAME` fields are now merged during pruning so the original calls are available in the final file. Sites surviving a pruning event now receive a flag in their `INFO` field called `RETAINED` so they can be identified in downstream steps.
- Added an option to `svtools lmerge` to retain genotype information during merging.
- Documentation on how to install via conda
- Updates to documentation and tutorial reflecting changes and including the new `svtools classify` command.
- Headers are now produced even when no variants are found. (Thanks to jasper1918)
- Numerous other fixes. Thank you to brunogrande and crazyhottommy for reporting issues.