Version 1.6.6499

Released on April 30th, 2024

Download at: https://download.jetbrains.com/biolabs/span/span-1.6.6499.jar

Changes:

• Faster SPAN model convergence by relative likelihood estimation
• Improved initialization to make SPAN more robust in low signal-to-noise ratio case
• Don't process contigs when coverage distribution is different from genome-wise
• Introduced --bg-sensitivity to configure sensitivity of peak backgrounds
• Dropped gap as obsolete
• Peaks from model procedure significantly improved tuning flexibility

Version 1.5.6351

Released on Feb 2nd, 2024

Download at: https://download.jetbrains.com/biolabs/span/span-1.5.6351.jar

Changes:

• Specify log file location with --log command line option
• Don't keep cache files until --keep-cache parameter is provided

Version 1.4.6197

Released on November 2nd, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.4.6197.jar

Changes:

Fixed problem with SPAN ignoring --threads command line argument

Version 1.3.5677

Released on July 20th, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.3.5677.jar

Changes:

• Fixed problem with paired end coverage loading and too long paired fragments

Version 1.2.5668

Released on June 27th, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.2.5668.jar

Changes:

• Improved peak calling for narrow marks histone marks
• Fixed beta value estimation for control correction on chromosome-filtered coverage
• Fixed problem with highly relaxed FDR settings

Version 1.1.5628

Released on March 9th, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.1.5628.jar

Changes:

• Bugfix update - fix problem with treatment and control scaling
• Upscale treatment and control library
• Slightly tweaked defaults - number of iterations and threshold till convergence
• Reverted compatibility with Java 8

v1.0.5604

Version 1.0.5604

Released on December 19, 2022

Download at: https://download.jetbrains.com/biolabs/span/span-1.0.5604.jar

Changes:

• Fixed problem load BAM file with some missing reads flags, e.g., mappingQuality
• Fixed beta values estimation - take into account bin size
• Set default bin size to 50bp
• Increased iterations to 50 and reduced convergence threshold to 0.1
• Added --clip option to increase peak positioning and density for narrow-shaped signal profiles
• Bugfixes

v1.0.5573

Version 1.0.5573

Released on October 12, 2022

Download at: https://download.jetbrains.com/biolabs/span/span-1.0.5573.jar

Changes:

• Switched to new procedure for computing peaks from HMM:
  1. Estimate HMM posterior error probabilities
  2. Pick candidate bins with relaxed posterior error probability, e.g. sqrt(fdr).
     This mitigates the problem of wide marks peaks split on strong fdrs.
  3. Using gap merge bins into candidate islands.
  4. Assign p-value to each island using based on combined p-values for blocks of consequent enriched bins.
     Each block is assigned P as average posterior log error probability for bins in blocks.
     50% top significant blocks scores are aggregated using length-weighted average as P for island.
  5. Compute qvalues on islands p-values, filter by alpha.
• Improved multistart initial NB states guess - use different params for each model
• Safeguard against infinite failures as initial guess for NB, which effectively converts NB to Poisson
• Reduced time required for peak calling
• Show progress while computing peaks from model
• Updated defaults values for SPAN peaks: fdr 0.05, gap 3
• Updated defaults for SPAN model: total iterations 20, log-likelihood threshold 1
• Added advanced SPAN model viewer
• Bugfixes

v0.13.5244

Version 0.13.5244

Released on Aug 12th, 2020

Fix logs formats
Download at: https://download.jetbrains.com/biolabs/span/span-0.13.5244.jar

0.12.0.5096

Version 0.12.0.5096

Released on Apr 22th, 2020

• Multistart for model fit
• Advanced model tuning parameters

Download at: https://download.jetbrains.com/biolabs/span/span-0.12.0.5096.jar