Altius/hotspot2

Issues

• scripts/hsmerge.sh creates empty files

  #29 opened 6 years ago by brianpenghe
  2

• Drosophila mappable regions

  #28 opened 6 years ago by brianpenghe
  1

• How can I get mappable region file?

  #27 opened 6 years ago by brianpenghe
  1

• line 102: starch: command not found

  #26 opened 6 years ago by brianpenghe
  4

• Need to fix edge case of score reporting in hsmerge.sh

  #23 opened 7 years ago by erynes
  1

• densities could have nan's

  #22 opened 8 years ago by sjneph
  1

• Bug in density file

  #21 opened 8 years ago by sjneph
  1

• Total cut counts, and SPOT, should be restricted to mappable cut counts when possible

  #19 opened 8 years ago by erynes
  1

• Field 5 of the hotspot output file needs to be an integer

  #20 opened 8 years ago by erynes
  1

• Per-base input to hotspot2.cpp gets collapsed when col5 = same; output should be too

  #17 opened 8 years ago by erynes
  6

• hotspot2.cpp: If MAxN = 0 at k_c and an incoming site has k << k_c, call findCutoff()

  #16 opened 8 years ago by erynes
  1

• hotspot2.cpp: If k < k_c lowers MAxN to 0, or k_c bin gets deleted, call findCutoff()

  #15 opened 8 years ago by erynes
  1

• hotspot2.cpp should allow the user to pass in a value for MAlength

  #14 opened 8 years ago by erynes
  1

• hotspot2 should allow for non-overlapping "inner windows" and a spectrum of overlap %

  #13 opened 8 years ago by erynes
  1

• hotspot2.cpp error/warning messages reporting offending regions should report chr too

  #12 opened 8 years ago by erynes
  1

• hotspot2.cpp needs to continue, not exit, when encountering a window with zero variance

  #11 opened 8 years ago by erynes
  1

• tallyCountsInSmallWindows.cpp assumes chromSizes file has 2 columns (not BED input)

  #10 opened 8 years ago by erynes
  1

• hotspot2.cpp: Inconsistency between using bin heights & moving avgs of them, also origDistnSize issue

  #9 opened 8 years ago by erynes
  1

• BRM::computePandFlush() needs to always call BRM::computeStats(-1)

  #8 opened 9 years ago by erynes
  1

• hotspot2.cpp erroneously calls SiteManager::getFDRvalsAndWriteAndFlush at end of BackgroundRegionManager::computePandFlush()

  #7 opened 9 years ago by erynes
  1

• Thou shalt not attempt log(0)

  #6 opened 9 years ago by erynes
  1

• Need non-uniquely-mappable locations

  #4 opened 9 years ago by sjneph
  1

• error when no fragments file is created

  #5 opened 9 years ago by sjneph
  1

• mktemp error

  #3 opened 9 years ago by sjneph
  1

• Underflow and/or rounding issues for very significant P-values

  #2 opened 9 years ago by erynes
  1

• no peaks

  #1 opened 9 years ago by sjneph
  2