To add support for a new reference genome, a user must do the following:
I emailed the author of SICER2 asking if it would be possible to implement any of the suggestions here. It is worth also noting, if one were to make these changes, one should also update the dtype set for chr. At the current moment, it is set to U6 or a unicode string of length 6, which may not be long enough in some edge-cases (could cause a string to get truncated and cause collisions).
For the time being, we will turn off sicer2 when the reference genome is rheMac10; however, we should explore other solutions if the author cannot implement this on their side:
Fork and add functionality described in issue 23
Fork, update sicer/lib/GenomeData.py with rheMac10 information and build docker image
SICER2 has information pertaining to genome chromosome lengths hard-coded in the following file: https://github.com/zanglab/SICER2/blob/master/sicer/lib/GenomeData.py
To add support for a new reference genome, a user must do the following:
I emailed the author of SICER2 asking if it would be possible to implement any of the suggestions here. It is worth also noting, if one were to make these changes, one should also update the
dtypeset forchr. At the current moment, it is set toU6or a unicode string of length 6, which may not be long enough in some edge-cases (could cause a string to get truncated and cause collisions).For the time being, we will turn off sicer2 when the reference genome is rheMac10; however, we should explore other solutions if the author cannot implement this on their side:
sicer/lib/GenomeData.pywith rheMac10 information and build docker image