Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

hmmsim only worked for Amino Acid models #117

Closed
traviswheeler opened this issue Dec 27, 2016 · 1 comment
Closed

hmmsim only worked for Amino Acid models #117

traviswheeler opened this issue Dec 27, 2016 · 1 comment
Milestone
3.1b2

Comments

@traviswheeler
Copy link
Contributor

ID h107
TITLE hmmsim only worked for Amino Acid models
AFFECTS 3.0 and later
FIXED_IN 3.1b2
STATUS CLOSED
XREF -
REPORTED_BY Marco Galardini marco.galardini@unifi.it
OPENED_DATE TJW, 16 Jan 2014
CLOSED_DATE TJW, 16 Jan 2014
DESCRIPTION
Running hmmsim on a DNA HMM produced the error:
"Error: HMM file tutorial/MADE1.hmm contains different alphabets"

An amino acid alphabet was assumed in the hmmsim implementation,
so an HMM with a DNA alphabet produced an error. Removed this
assumption - now the alphabet is determined from the HMM.
@traviswheeler traviswheeler added this to the 3.1b2 milestone Dec 27, 2016
@cryptogenomicon
Copy link
Member

This fix was incorrect. It left alphabet in an undefined state and can cause hmmsim to segfault. Fixed in b81f847.

cryptogenomicon added a commit that referenced this issue Jun 2, 2018
@cryptogenomicon
Fixes the fix for issue #117; hmmsim segfault.
b81f847 
The fix for iss#117 was incorrect. It left hmmsim's alphabet
undefined, which could cause segfaults.

Also adds new tests to the testsuite.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
3.1b2
Development

No branches or pull requests
2 participants
@traviswheeler @cryptogenomicon