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Updated benchmark #156

Merged
merged 76 commits into from
Jun 7, 2024
Merged

Updated benchmark #156

merged 76 commits into from
Jun 7, 2024

Commits on Jun 4, 2024

  1. Version bump COJAC 0.9.2

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Commits on Jun 7, 2024

  1. [method] cliquesnv with output snvs -- create empyt file if cliquesnv… 

    … is not outputting anything
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  2. exclude shorah_amplicon since it fails on the illumina populations du… 

    …e to an error in b2w
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  3. vary population parameters and coverage

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  4. subsample hiv mix

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  5. exlcude viloca_multi since the cluster allocation of multiple threads… 

    … sort of didn't work
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  6. add rerun-triggers mtime snakemake command

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  7. [viloca] set higher win_min_ext threshold for 10-IAV-mix

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  8. updates

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  9. conda enviroment

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  10. viloca with older configuration

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  11. exclude indels configuration for now

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  12. PVY mix with uniform tiling

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  13. add another sars-mix

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  14. update resources

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  15. add older viloca configuration

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  16. more methods + updated populations

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  17. run indel also

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  18. rename methods, since bash takes files names of length max 255

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  19. method names updated

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  20. method names updated

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  21. b2w multi

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  22. fix: in case no mutations are in vcf

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  23. [update] distance populations for conference figures

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  24. [viloca method] also report posterior of haplotypes

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  25. [varyvilocaparams] update config and params

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  26. [realdata] don't use SARS-CoV-2-Two-Strain-Mix -- since we don't have… 

    … the full ground truth
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  27. [HIV-5-mix] update ground truth - exclude deletions since they are no… 

    … biological deletions but rather due to incomplete reference strains
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  28. [single_bed_file] fix

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  29. [single_bed_file] fix int

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  30. [performance_global] save posterior of predictions

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  31. [method_def] viloca with posterior threshold

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  32. [method_def] viloca with posterior threshold

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  33. [experimental data] 5-virus-mix correct ground truth

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  34. [local_haplo] add predicthaplo

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  35. add method: strainline

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  36. update method strainline

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  37. update method strainline

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  38. remove rules for 2 strain sars-cov2 mix

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  39. add predicthaplo

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  40. remove old methods that are not used anywhere

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  41. correct output name for different applications and improved comments

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  42. [shorah] reduce window size for illumina samples

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  43. [fix] simulation of deletions and insertions into the haplotypes

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  44. [add] extra performance measures for local_haplo_setup

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  45. fix illumina simulation with indels in haplotypes, bwa is not alignin… 

    …g them correctly, hence use minimap2
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  46. fix indel simulation, ground truth table, simulate missing codon or i… 

    …nserted codon
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  47. [remove] rule to provide curlcakes ont data

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  48. [remove] rule to provide wastewater sars-cov2 data

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  49. [remove] rule to provide wastewater sars-cov2 data

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  50. [remove] rule to provide wastewater sars-cov2 data

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  51. [remove] rule to provide wastewater sars-cov2 data

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  52. [fix groud truth list for distance haplo generation]

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  53. [clean-up] ground_truth_corrected.csv not neeeded anymore, since grou… 

    …nd_truth.csv was fixed
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  54. config_distance: final version as in manuscript

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  55. remove cliquesnv version that returns snvs wrt consensus seq

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  56. distance config: final methods

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  57. remove corrected groundtruth file

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  58. final methods list and simulated dataset for varyvilocaparams

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  59. realdata update to final method versions

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  60. call indels

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  61. remove outdated methods

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  62. method_definitions: cliquesnv

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  63. update method defintions as run on cluster

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  64. generate haplotypes: correct deletion position in ground truth

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  65. [local_haplo_setup] add readme

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  66. fix indel ground truth and performance evaluationa

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  67. fix indel ground truth and performance evaluationa

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  68. indel config

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  69. remove isfile() tst

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  70. update viloca ewm for amplicon

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  71. add indel settings and performance eval

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  72. typo

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  73. [real data] complete insert file

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  74. [add] notebooks for figures in manuscript

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  75. Keep the linter happy

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