Altius hotspot2 issues - Githubissues

Altius / hotspot2

Implementation of hotspot2 by Eric Rynes

16 stars 3 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

scripts/hsmerge.sh creates empty files

#29 brianpenghe closed 5 years ago
2
Drosophila mappable regions

#28 brianpenghe closed 5 years ago
1
How can I get mappable region file?

#27 brianpenghe closed 5 years ago
1
line 102: starch: command not found

#26 brianpenghe closed 5 years ago
4
Dockerize

#25 fwip opened 6 years ago
0
Dev v2.0

#24 erynes closed 6 years ago
0
Need to fix edge case of score reporting in hsmerge.sh

#23 erynes closed 7 years ago
1
densities could have nan's

#22 sjneph closed 7 years ago
1
Bug in density file

#21 sjneph closed 7 years ago
1
Field 5 of the hotspot output file needs to be an integer

#20 erynes closed 8 years ago
1
Total cut counts, and SPOT, should be restricted to mappable cut counts when possible

#19 erynes closed 8 years ago
1
Merge hotspot2.cpp output

#18 fwip closed 8 years ago
0
Per-base input to hotspot2.cpp gets collapsed when col5 = same; output should be too

#17 erynes closed 8 years ago
6
hotspot2.cpp: If MAxN = 0 at k_c and an incoming site has k << k_c, call findCutoff()

#16 erynes closed 8 years ago
1
hotspot2.cpp: If k < k_c lowers MAxN to 0, or k_c bin gets deleted, call findCutoff()

#15 erynes closed 8 years ago
1
hotspot2.cpp should allow the user to pass in a value for MAlength

#14 erynes closed 8 years ago
1
hotspot2 should allow for non-overlapping "inner windows" and a spectrum of overlap %

#13 erynes closed 8 years ago
1
hotspot2.cpp error/warning messages reporting offending regions should report chr too

#12 erynes closed 8 years ago
1
hotspot2.cpp needs to continue, not exit, when encountering a window with zero variance

#11 erynes closed 8 years ago
1
tallyCountsInSmallWindows.cpp assumes chromSizes file has 2 columns (not BED input)

#10 erynes closed 8 years ago
1
hotspot2.cpp: Inconsistency between using bin heights & moving avgs of them, also origDistnSize issue

#9 erynes closed 8 years ago
1
BRM::computePandFlush() needs to always call BRM::computeStats(-1)

#8 erynes closed 8 years ago
1
hotspot2.cpp erroneously calls SiteManager::getFDRvalsAndWriteAndFlush at end of BackgroundRegionManager::computePandFlush()

#7 erynes closed 8 years ago
1
Thou shalt not attempt log(0)

#6 erynes closed 8 years ago
1
error when no fragments file is created

#5 sjneph closed 8 years ago
1
Need non-uniquely-mappable locations

#4 sjneph closed 8 years ago
1
mktemp error

#3 sjneph closed 8 years ago
1
Underflow and/or rounding issues for very significant P-values

#2 erynes closed 8 years ago
1
no peaks

#1 sjneph closed 8 years ago
2