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

CompareSAMs sometimes reports a file as being different from itself #160

Closed
mattsooknah opened this issue Feb 13, 2015 · 0 comments
Closed

CompareSAMs sometimes reports a file as being different from itself #160

mattsooknah opened this issue Feb 13, 2015 · 0 comments
Assignees
@mattsooknah
Labels
bug

Comments

@mattsooknah
Copy link
Contributor

Suppose you have a coordinate-sorted file foo.sam with multiple entries having the same read name and start coordinate (for whatever reason). Calling CompareSAMs foo.sam foo.sam will tell you that foo.sam differs from itself!

This is because the code currently assumes that we only have one entry for each read name at a given coordinate. Moreover, it traverses the "left" and "right" files asymmetrically, so that duplicate entries will get respected in one file but not the other.
@mattsooknah mattsooknah self-assigned this Feb 13, 2015
@mattsooknah mattsooknah mentioned this issue Feb 13, 2015
Closed
@nh13 nh13 closed this as completed Mar 6, 2015
@akiezun akiezun mentioned this issue Apr 21, 2015
Closed
@mattsooknah mattsooknah mentioned this issue Sep 16, 2015
Closed
@yfarjoun yfarjoun mentioned this issue Apr 16, 2016
Merged
yfarjoun pushed a commit that referenced this issue Apr 17, 2016
Fixed bug in CompareSams that occurs when two read mates have the sam…
e54c655 
…e genomic start position. (#516)

Previously this would show up as "missing left" since the key was read-name and position and the first read would be overwritten by the second. Now I also include "first" or "second" in the key and this solves the problem.

- added a test that previously failed.

- fixed a test that was broken with fix. since the key now includes first/second in pair, it was needed that these match up between the two files for the test.

- resolves #160 
- resolves #284
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@mattsooknah mattsooknah

Labels
bug
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@nh13 @mattsooknah