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Changelog

v0.38.0 (2022-11-27)

Feature

Fix

v0.37.1 (2022-11-04)

Fix

v0.37.0 (2022-10-28)

Feature

Fix

v0.36.2 (2022-10-27)

Fix

  • Fix minor issue with mix of forward-only and normal in dashboard (4d44f16)

Documentation

v0.36.1 (2022-10-27)

Fix

  • Update web address in dashboard (451a4ff)

Documentation

  • Update readme live dashboard link (b73b141)

v0.36.0 (2022-10-25)

Feature

  • Add MAP version of dashboard as well (849c13e)
  • Update variable names (a87e712)

v0.35.7 (2022-10-17)

Fix

  • Stop immediately after keyboard interruption (157e9f0)

v0.35.6 (2022-10-17)

Fix

  • Fix issue in dashboard when only forward samples (288f24b)

v0.35.5 (2022-10-17)

Fix

  • Remove empty data before fitting (94d7975)

v0.35.4 (2022-10-17)

Fix

  • Do not overwrite previous config-file when auto suffix (5b370dc)
  • Automatically add suffix to config-file (75fcb19)

v0.35.3 (2022-10-17)

Fix

  • Allow forward-only and normal in same dashboard (4acbe05)

v0.35.2 (2022-10-14)

Fix

  • Add variables to forward only (ff737b7)

v0.35.1 (2022-10-12)

Fix

  • Improve dashboard for significance (3d731d1)

v0.35.0 (2022-10-12)

Feature

  • Update dashboard to new fit main metric (2ed91fb)

v0.34.0 (2022-10-10)

Feature

  • Add significance as main fit quality (be20230)

v0.33.5 (2022-10-05)

Fix

v0.33.4 (2022-10-04)

Fix

v0.33.3 (2022-10-03)

Fix

  • Fix issue in Dashboard when k_sum is zero (2379728)

v0.33.2 (2022-10-02)

Fix

v0.33.1 (2022-10-02)

Fix

  • Fix divide by zero error in non CT/GA mismatc (3bae3c6)

v0.33.0 (2022-09-30)

Feature

  • Add non_CT_GA_damage_frequency (ea18e7a)

v0.32 (2022-09-14)

Feature

  • Add CI interval to dashboard (7e1653f)

Fix

  • Sort samples in dashboard automatically (2bb0bd0)
  • Fix Futurewarning in new Pandas version (c918ca5)
  • Improve error message when unsorted bam file (1d53682)
  • Fix issue when metaDMG binary does not exist (3c949be)
  • Add D-max to dashboard (dcfe019)

v0.31 (2022-09-07)

Feature

  • Improve Bayesian priors (1ad7c82)

Fix

  • Allow for larger values in dataframe counts (1fc9db1)
  • Improve progress bar for Bayesian runs (5ee0aa5)
  • Improve speed of Bayesian confidence interval (c4585f7)

v0.30 (2022-09-06)

Feature

  • Update priors to be more conservative (cb98015)

Fix

  • Improve multiprocessing api (e196a53)

v0.29 (2022-09-04)

Feature

  • Add confidence intervals to Bayesian model (38c95d5)

Fix

  • Use approximate conf. intervals for bayesian (e92f298)

v0.28 (2022-08-12)

Feature

  • Better fits for low-damage groups (793ffff)

Fix

  • Fix issue with logging in parallel (9e065aa)
  • Improve logging messages (7a35b3a)
  • Handle empty data and better error handling (f2d27ff)
  • Catch metaDMG-cpp error with unsorted files (7c42082)
  • Improve Bayesian D_max when few reads (35d7247)
  • Improve low-damage fits (838143b)

Documentation

  • Add docstring to workflow function (2ee4c6b)
  • Update the docstring for the PMD command (102f7aa)

v0.27 (2022-07-15)

Feature

  • Add config-gui to CLI (672fea7)
  • Use Rich with Typer for pretty CLI (3a960a5)

Fix

  • Fix PMD command handle errors and output csv (84c002f)
  • Add groups to CLI (8762292)
  • Update dependencies (2f91c56)
  • Update dependencies (299a6c4)

Documentation

  • Update PMD command (9bb6382)
  • Update config-gui image in docs (9700d88)
  • Add config-gui image to docs (e62e603)
  • Include config-gui in docs (480f813)

v0.26 (2022-07-04)

Feature

  • Add minimum reads as an optional threshold (23f9c16)

Fix

  • Change alignment file in test dir (2beed66)

Documentation

  • Add min-reads to onoine docs (0f74800)

v0.25.0 (2022-07-04)

Feature

  • Disallow the usage of similarity scores and edit distances at the same time (bf7f941)

Fix

  • Re-raise errors (9b08e76)
  • Add better error message in the of unspecified custom database (a711a01)

v0.24 (2022-06-14)

Feature

  • Add PMD command and include Configs in core (11eab19)

Fix

  • Change "nreads" in non-LCA stats to N_alignments (85c033c)
  • Fix bug with mismatch-to-mapDamage when forward-only mode (89670fa)
  • Update dependencies (206c47b)
  • Allow mismatch_to_mapDamage to work with forward-only data (c59240f)
  • Fix issue when using --add-fit-predictions together with forward_only (6c0126c)
  • Fix issue with forward-only in dashboard (7d5310f)
  • Improve marks in dashboard (f105fcf)
  • Allow for compressed files in convert. (aebdbff)
  • Infer metaDMG-cpp from config file in PMD (f38e3c6)
  • Include static folder in docs (dcbcfd9)
  • Continue to use Union in Python 3.9 (2a04213)
  • Update lock file (ecec382)

Documentation

v0.23 (2022-03-29)

Feature

Fix

  • Update old configs in convert and filter CLI (c7fad7c)

Documentation

  • Add more advanced tutorial (KapK) (8596c43)
  • Add github pages action (d2a5b7f)
  • Update CLI doc (5ad0851)
  • Add mermaid diagram to tutorial (93ac0c0)

v0.22 (2022-03-28)

Feature

  • Add --overwrite as option in config (f73bda3)
  • Add D_max significance and variance_scaling (4c5f7f7)
  • Add test data to package (a522623)

Fix

  • Test CI-CD workflow (02636a9)
  • Add tqdm to viz (87f670b)
  • Update tests (f3ab9ae)
  • Inlcude helper functions in metaDMG.main (e8fc27d)
  • Auto-update old config files, but raise warning (b3b8f32)
  • Check BAM size (982d2d4)
  • Use dependency groups for dev tools (e1c010a)
  • Pre-commit (b1fd695)

Documentation

  • Include Python version in the requirements (ced545b)

v0.21 (2022-03-17)

Feature

  • Merge viz (dashboard) (28e56bc)
  • Add slimmer base install of metaDMG (with fit, viz, and all as extras) (75b4ecc)
  • Change default install (d8cc434)
  • Make fitting part of package optional (5efd447)

Fix

  • Try to fix action (6c736a0)
  • Fix actions (e1e6e8d)
  • Disable auto-reloading in dashboard to allow for debugging (8a4e845)
  • Move CLI-related code to cli folder (6ad0293)

v0.20 (2022-03-16)

Feature

  • Update dashboard to also work with non-LCA (0495d81)
  • Allow for non-LCA mode (2bd5901)

Fix

  • Update dependencies (inlcuding dashboard= (003e0c8)
  • Fix issue with dashboard and old parquet files (0506d5a)
  • Improve Paths parsing (1ab3cd1)
  • Parse metaDMG-cpp path as str (0943a29)
  • Fix error with attrs / dataclass (8a507b9)
  • Use Python v3.9 (b93d97c)
  • Fix error with mapDamage formats (c8746ce)
  • Fix parsing with metaDMG-lca binary (f69e5f0)
  • Fix error with Path and metaDMG-lca (c7a57c1)
  • Adding type hints, rewrite config files and adding confirmation prompt (a046687)
  • Make all tax_ids to strings (fc1fee4)

Documentation

v0.19 (2022-03-09)

Feature

Fix

  • Update dashboard to allow the use of forward-only (35eeebc)

Documentation

  • Update readme to reflect the forward-only use (5f0e760)
  • Update changelog (b32a0dd)

v0.18 (2022-03-08)

v0.17 (2022-03-08)

  • Add damage-mode "local" or "global" as options (5e153bb)
  • Make --names, nodes and acc2tax mandatory for LCA but not for local and global (b2ae2a2)
  • Improve readme regarding non-LCA mode (bbb36b5)
  • Add temporary folders for LCA (21201c7)
  • Update logger-tt dependency (30814f7)
  • Update logging port (e193985)
  • Update metaDMG_viz (48b1838)
  • Add jackknife possibility for computing z error (a486431)
  • Update dependencies (a1d04e3)
  • Fix bug when concatenating two dataframes when appending fit predictions (ac3bd67)
  • Fix CLI bug (d8c1dee)
  • Update docs to reflect update in metadamage (72b055f)

v0.16 (2022-02-02)

  • Remove error when parsing taxes with apostrophe in tax name (e0e0405)
  • Also remove lca.gz files (a8dbf91)
  • Update dependencies for M1 macs (5f80629)

v0.15 (2022-01-31)

  • Add the option to include the fit predictions in the output csv files (a12d585)
  • Read .gz zipped files (639873b)
  • Update dependencies (33f46fb)
  • Update docs (202d484)

v0.14 (2022-01-05)

  • Update dependencies (including metaDMG-viz) (ed281e5)

v0.13 (2021-11-10)

  • Add --long-name as bool flag to CLI (b2b64cb)
  • Fix error when not doing progressbar in parallel Bayesian fits (097785a)
  • Make update (f249210)
  • Add try except for MismatchFileError (76cc35c)
  • Add MismatchFileError for when mismatch.txt has error (a8662b0)
  • Fix error with forced and multiprocessing (fc8e4e0)
  • Improve changelog (a065411)
  • Limit number of cores to be maximum the number of configs (60e4d92)
  • Add forced option to compute (ef01915)
  • Add sample and tax_id information to the fits (c308262)
  • Remove Tax IDs with k_sum_total == 0 (5ec3058)
  • Delete files on KeyboardInterupt (clean up) (89d962b)
  • Add hidden lines in log file and handle return code better (1762667)
  • Improve error logging and messages for metadamage-cpp (73068ed)
  • Add mapDamage conversion command (b808fcd)
  • Remove .bin files (c16364d)
  • Fix error with bad fits and mask them invalid (dd58c6c)
  • Update dashboard and include online example of dashboard (39ef8bb)
  • Add small fix to deal with old mismatch files that uses the old notation (|z| instead of |x|) (4093b0f)
  • Improve frequentists fits for forward and reverse fits (735d25c)
  • Fix ImportError in NumPyro (8245c57)
  • Add metaDMG version to logging (12d968a)
  • Add interactive dashboard to readme (61f3116)
  • Add --forced to readme (12a2114)
  • Include mismatch-to-mapDamage in readme (29cbcf9)
  • Update readme with how to update (753b360)

v0.12 (2021-09-30)

  • Update Dashboard to include pdf-plots and progressbar, and update Dash and dbc (fbf727c)
  • Add better handling of fit errors (4facb88)
  • Add progress bars when running single files or with a single core (11c8cdb)
  • Improve error logging while fitting (cce13ab)
  • Memory leak of bayesian modelling (d04f5a8)
  • Log errors to see where they occur and skip them for now. (40d0387)
  • Allow running for old config files without cores_per_fit being set (9a07f83)
  • Add "cores-per-sample" as config parameter (0a26847)

v0.11 (2021-09-20)

  • Use random ports for logging to decrease risk of reusing same port (200eecc)
  • Allow for multiple loggers (multiple jobs) (0ee5ce0)
  • Make null model more similar to damage model (74d575e)
  • Refactor dashboard to only take a results dir as input (26608bb)
  • Better parsing of read mode vs contig mode (06e3039)

v0.10 (2021-09-16)

  • Add Bayesian computation of rho_Ac (db61f5d)
  • Add uncertainty estimates to Bayesian results (21e81c7)
  • Improve error messages for Bayesian fits (4e7beba)

v0.9 (2021-09-13)

  • Include fitting as part of main package (14c2b7c)
  • Remove MetaDMG-cpp from github (bc5bd05)