/adam

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.

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

Phred values from 156–254 do not round trip properly between log space #1964

Closed
fnothaft opened this Issue Mar 23, 2018 · 0 comments

Comments

Assignees

@fnothaft fnothaft

Labels
bug
Projects
None yet
Milestone
  0.24.0
1 participant
@fnothaft
@fnothaft
Member

fnothaft commented Mar 23, 2018

No description provided.

@fnothaft fnothaft added the bug label Mar 23, 2018

@fnothaft fnothaft added this to the 0.24.0 milestone Mar 23, 2018

@fnothaft fnothaft self-assigned this Mar 23, 2018

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 23, 2018

@fnothaft
[ADAM-1964] Lower point where phred conversions are done using log code. 
Resolves bigdatagenomics#1964. There was an underflow somewhere causing round trip from
log space values to Phred to mismatch for values between 164 and 254.
This change lowers the point where we switch from using the precomputed
table to where we use the log math. Also, we add a unit test checking
round trip values using PhredUtils.
394f9f6

@fnothaft fnothaft referenced this issue Mar 23, 2018

Merged

[ADAM-1964] Lower point where phred conversions are done using log code. #1965

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 23, 2018

@fnothaft
[ADAM-1964] Lower point where phred conversions are done using log code. 
Resolves bigdatagenomics#1964. There was an underflow somewhere causing round trip from
log space values to Phred to mismatch for values between 164 and 254.
This change lowers the point where we switch from using the precomputed
table to where we use the log math. Also, we add a unit test checking
round trip values using PhredUtils.
03054f2

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 23, 2018

@fnothaft
[ADAM-1964] Lower point where phred conversions are done using log code. 
Resolves bigdatagenomics#1964. There was an underflow somewhere causing round trip from
log space values to Phred to mismatch for values between 164 and 254.
This change lowers the point where we switch from using the precomputed
table to where we use the log math. Also, we add a unit test checking
round trip values using PhredUtils.
eea8864

@heuermh heuermh closed this in #1965 Mar 23, 2018

heuermh added a commit that referenced this issue Mar 23, 2018

@fnothaft @heuermh
[ADAM-1964] Lower point where phred conversions are done using log code. 
Resolves #1964. There was an underflow somewhere causing round trip from
log space values to Phred to mismatch for values between 164 and 254.
This change lowers the point where we switch from using the precomputed
table to where we use the log math. Also, we add a unit test checking
round trip values using PhredUtils.
c15b129
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment