| 2024-05-08 |
philippadoherty | require nuc-open-nuc region len > openregion_minlen
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commit | commitdiff | tree |
| 2024-05-02 |
philippadoherty | deal with nuc-open-nuc-open-nuc type regions
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commit | commitdiff | tree |
| 2024-05-02 |
philippadoherty | correct 'open' start/end pos
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commit | commitdiff | tree |
| 2024-05-02 |
philippadoherty | use narrowPeak instead of gappedPeak
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commit | commitdiff | tree |
| 2024-04-26 |
philippadoherty | revert predicted_proba_file
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commit | commitdiff | tree |
| 2024-04-26 |
philippadoherty | Merge branch 'feat/macs3/memory_consumption' of https...
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commit | commitdiff | tree |
| 2024-04-26 |
philippadoherty | temp change predicted_proba_file def
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commit | commitdiff | tree |
| 2024-04-12 |
philippadoherty | change generate_states_path logic
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commit | commitdiff | tree |
| 2024-04-12 |
philippadoherty | try again
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commit | commitdiff | tree |
| 2024-04-12 |
philippadoherty | fix generate_states_path function
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commit | commitdiff | tree |
| 2024-04-12 |
philippadoherty | try saving to bedgraph
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commit | commitdiff | tree |
| 2024-04-12 |
philippadoherty | read bytes
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commit | commitdiff | tree |
| 2024-04-11 |
philippadoherty | try save_proba_to_bedGraph
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commit | commitdiff | tree |
| 2024-04-11 |
philippadoherty | include debugging comments, write vars then stop
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commit | commitdiff | tree |
| 2024-04-10 |
philippadoherty | clean misc vars
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commit | commitdiff | tree |
| 2024-03-26 |
philippadoherty | Include pushes to master - Merge branch 'master' into...
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commit | commitdiff | tree |
| 2024-03-15 |
philippadoherty | retry hmmratac cmdline tests
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commit | commitdiff | tree |
| 2024-03-15 |
philippadoherty | add back in extra hmmratac cmdline tests
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commit | commitdiff | tree |
| 2024-03-15 |
philippadoherty | add --hmm-type option for poisson or gaussian hmm
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commit | commitdiff | tree |
| 2024-03-14 |
philippadoherty | try removing other hmmratac standard results
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commit | commitdiff | tree |
| 2024-03-14 |
philippadoherty | try cmdlinetest with poisson output
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commit | commitdiff | tree |
| 2024-03-14 |
philippadoherty | change hmm model to poisson, change ret_training_data...
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commit | commitdiff | tree |
| 2024-03-13 |
philippadoherty | add test for hmm poisson
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commit | commitdiff | tree |
| 2024-02-27 |
philippadoherty | update standard prediction results
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commit | commitdiff | tree |
| 2024-02-27 |
philippadoherty | Merge branch 'master' into feat/macs3/unittest_hmm
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commit | commitdiff | tree |
| 2024-02-27 |
philippadoherty | update startprob
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commit | commitdiff | tree |
| 2024-02-27 |
philippadoherty | update standard model values
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commit | commitdiff | tree |
| 2024-02-27 |
philippadoherty | print model values
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commit | commitdiff | tree |
| 2024-02-27 |
philippadoherty | Merge branch 'feat/macs3/unittest_hmm' of https://github...
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commit | commitdiff | tree |
| 2024-02-17 |
philippadoherty | init updated hmm unittest
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commit | commitdiff | tree |
| 2024-02-16 |
philippadoherty | init updated hmm unittest
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | define venv w/o py version, pip install
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | try pip install
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | try alt pip install
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | Merge branch 'feat/macs3/test_peak_overlap' of https...
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | try simpler pip install via requirements.txt
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commit | commitdiff | tree |
| 2024-02-13 |
Philippa Doherty | Merge pull request #618 from macs3-project/doc/macs3...
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | try again ubuntu22.04
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | try again ubuntu22.04
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | try ubuntu-22.04
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | try debian bookworm
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | test nonx64
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | test nonx64 with py 3.11, numpy 1.24
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | test non x64, numpy 1.25
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | change non x64 py version to 3.11, numpy 1.24
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | numpy 1.25 w/o py 3.12
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | numpy 1.24 w/o py 3.12
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | numpy 1.25 py 3.11
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commit | commitdiff | tree |
| 2024-02-13 |
philippadoherty | test numpy 1.25 w/o py 3.12
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commit | commitdiff | tree |
| 2024-02-12 |
philippadoherty | test numpy==1.25
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commit | commitdiff | tree |
| 2024-02-12 |
philippadoherty | test numpy==1.24
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commit | commitdiff | tree |
| 2024-01-10 |
philippadoherty | bring branch up to speed from last PR Merge branch...
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commit | commitdiff | tree |
| 2024-01-10 |
philippadoherty | remove cython from setup.py requirements
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commit | commitdiff | tree |
| 2024-01-10 |
philippadoherty | fix labels for signals
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commit | commitdiff | tree |
| 2023-11-28 |
philippadoherty | fix inlineMath vs displayMath
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commit | commitdiff | tree |
| 2023-11-22 |
philippadoherty | minor changes to contributing
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commit | commitdiff | tree |
| 2023-11-21 |
philippadoherty | change equation wrappers to double $$
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commit | commitdiff | tree |
| 2023-11-16 |
philippadoherty | add mathjax configuration and jekyll plugin
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commit | commitdiff | tree |
| 2023-11-02 |
Philippa Doherty | fix callvar verbose
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | reorder hmmratac options
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | add hmmratac options
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | add windows note
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | fix command line options
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | try paths-ignore again
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | try paths-ignore
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | try branches-ignore
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | try disable test again
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | test workflow with 'docs' branch
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commit | commitdiff | tree |
| 2023-11-02 |
philippadoherty | edit .md command line options
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commit | commitdiff | tree |
| 2023-07-20 |
philippadoherty | fix callvar arguments
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commit | commitdiff | tree |
| 2023-07-14 |
philippadoherty | fix hmmratac tests 15, 15.1, 15.2
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commit | commitdiff | tree |
| 2023-07-14 |
philippadoherty | add standard_results for --model and -t options
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commit | commitdiff | tree |
| 2023-07-12 |
philippadoherty | add 15.1 and 15.2 hmmratac tests
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commit | commitdiff | tree |
| 2023-07-12 |
philippadoherty | clean up
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commit | commitdiff | tree |
| 2023-07-12 |
philippadoherty | rm peaks.sort
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commit | commitdiff | tree |
| 2023-07-12 |
philippadoherty | fix input for init_from_PeakIO
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commit | commitdiff | tree |
| 2023-07-12 |
philippadoherty | add conditions for -modelonly, -t
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commit | commitdiff | tree |
| 2023-07-12 |
philippadoherty | add -t and --modelonly
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commit | commitdiff | tree |
| 2022-09-30 |
philippadoherty | Merge branch 'feat/macs3/hmmratac' of https://github...
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commit | commitdiff | tree |
| 2022-09-30 |
philippadoherty | update unittest
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commit | commitdiff | tree |
| 2022-09-15 |
philippadoherty | change unittest
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commit | commitdiff | tree |
| 2022-09-15 |
philippadoherty | round transmat_ to 4 decimals
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commit | commitdiff | tree |
| 2022-07-19 |
philippadoherty | rename options.hmm_binsize if hmm_model_init used
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commit | commitdiff | tree |
| 2022-07-19 |
philippadoherty | save binsize to model
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commit | commitdiff | tree |
| 2022-07-19 |
philippadoherty | include region definition in hmm_model_init
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commit | commitdiff | tree |
| 2022-07-19 |
philippadoherty | move hmm_model_init to HMMR_HMM
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commit | commitdiff | tree |
| 2022-07-19 |
philippadoherty | add n_features
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commit | commitdiff | tree |
| 2022-07-18 |
philippadoherty | added model parser (needs work)
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commit | commitdiff | tree |
| 2022-06-10 |
philippadoherty | try different minlen condition
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commit | commitdiff | tree |
| 2022-06-10 |
philippadoherty | add minlen option to save_accessible_regions
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commit | commitdiff | tree |
| 2022-06-10 |
philippadoherty | fix index out of range in save_accessible_regions
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commit | commitdiff | tree |
| 2022-06-09 |
philippadoherty | rm if accessible_regions < 3
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commit | commitdiff | tree |
| 2022-06-09 |
philippadoherty | fix index out of range in save_accessible_regions
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commit | commitdiff | tree |
| 2022-06-09 |
philippadoherty | deal with regions < 3
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commit | commitdiff | tree |
| 2022-06-07 |
philippadoherty | generate_states_path fix start_pos
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commit | commitdiff | tree |
| 2022-06-07 |
philippadoherty | except ValueError with faulty means, stddevs
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commit | commitdiff | tree |
| 2022-06-03 |
philippadoherty | change to sorted(chrnames)
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commit | commitdiff | tree |
| 2022-06-03 |
philippadoherty | changed broadpeak for loop range
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commit | commitdiff | tree |
| 2022-05-26 |
philippadoherty | changed format of block_sizes, block_starts
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commit | commitdiff | tree |
| 2022-05-25 |
philippadoherty | correct candidate_bins start and end_pos
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commit | commitdiff | tree |
