demo notebook update, config update, tests update

* moving docs from wiki to git

* fix more image references

* fix more links

* added pip install instructions

* change command line to use the insilicosv CLI entry point.  remove docs about deleted scripts generate_synthetic_genome.sh and divergent_repeat_augmentation.sh

…able script

Added conda environment for running the demo notebook

…nstructions

docs: README.md install instructions changed to use pip or bioconda

README updates (directory setup for user)

…pped transformed ref to original ref

* demo notebook update, config update, tests update

* PR updates to demo notebook

* move wiki to git (#1)

* moving docs from wiki to git

* fix more image references

* fix more links

* added pip install instructions

* change command line to use the insilicosv CLI entry point.  remove docs about deleted scripts generate_synthetic_genome.sh and divergent_repeat_augmentation.sh

* removing install/ dir for now, obsoleted by pip install (#2)

* .gitignore: added notebook outputs

* update version to 0.0.5

* move license to pyproject.toml

* demo notebook fixes

* adding demo notebook conda env definition

* change pbsim3 model path

* insilicosv-demo-env: added minimap2

* use pbsim3 model from the pbsim3 conda package

* added igv to demo notebook conda env

* made simulated read coverage configurable in demo notebook via env vars

* update demo notebook env to current igv

* fix env name

* .gitignore: add IGV_screenshots

* adding the original definition of insilicosv-demo-env

* .gitignore: added workflow-related ignores

* docs: README.md install instructions changed to use pip or bioconda

* change references to simulate.py into references to insilicosv executable script

* added demo notebook instructions

* docs: README.md -- clarified where to find config file syntax

* fixed image link for the grammar

* added space around image ref

* added more spaces around image refs to ensure correct display on github

* removed divergent repeat example visualization

* README updates (directory setup for user)

* removed, for now, documentation reference to the utility code that mapped transformed ref to original ref

* removed get_original_base_pos() from utils.py for now

* removed div_repeat_postproc

* doc: remove stray line

* docs: remove duplicate line

* docs: drop mention of wiki

* docs: removed mentions of not-yet-released functionality

---------

Co-authored-by: crohlicek <[email protected]>
Co-authored-by: Chris Rohlicek <[email protected]>

* updates to docs

* info about rel/abs path for reference in config

* INDEL support mentioned, default sim settings removed from example configs

* added small config example to input_guidelines page

* mention of SVs replaced with variants in places where SNPs are meant to be included

* example config in input_guidelines changed to use lists for input sizes

* remove statement of rel/abs ref path; include mention of output insertions.fa file

* clarifying terminology

* moving summary config github gist to dedicated .md file in docs/

* link to example_use_cases.md given with more explanation

* adding mention of ref as config input

* included descriptions of all config inputs with links to examples in input format description

* removed usage of order in output bed format, and changed nth_sv to sv_id

* removed unused code

* adding back internal logic for order

* config now accepts min_lengths and max_lengths inputs of type list only

* updated demo config to use lists for input sizes

* example_use_cases.md updated with configs that use lists for input sizes

* avoid_intervals moved to top level of confi

* SVs config field replaces with variant_sets; related changes to docs and tests

* clarified config file format

* fix to old default stored for filter_small_chr

* removal of forced HOM for div_dDUPs (a requirement for div. repeats)

---------

Co-authored-by: Ilya Shlyakhter <[email protected]>

* updates / typo corrections to demo notebook markdown cells

* change description of PBSIM read combination step

…into develop

…nv.yml, since our docs say to use the platform-agnostic insilicosv-demo-env.reqs.txt

…version of insilicosv but bioconda does not yet