v0.3.2

Bug Fixes

In Version 0.3.1 parseIntaRNA.py was modified to reduce the RAM usage of parsing IntaRNA CSV result file, i.e. parsed and saved IntaRNA predicted binding sites in chunks, but later found that modification did not fix the RAM usage issue. Now in this release the bug introduced in v0.3.1 has been fixed, and now the RAM usage is under control even when processing very large IntaRNA CSV result file

v0.3.1

Updates

1. modify parseIntaRNA.py to reduce the RAM usage of parsing IntaRNA CSV result file, i.e. parse and save IntaRNA predicted binding sites in chunks

v0.3.0

Updates

1. Update Enclosed IntaRNA version from 3.1.3 to 3.3.1
2. Change IntaRNA prediction mode from Exact --mode=M to default Heuristic --mode=H, and add an option --outOverlap=Q to allow predicted multiple suboptimal binding sites overlapping in query tRF sequence, but not overlapping in target RNA sequence

v0.2.1

Bug Fixes

1. Fix a bug that numeric tRF ID and/or transcript ID will cause error

v0.2.0

Updates

1. Delete P_Val column in the 3 output prediction CSV files.
2. Add a Consensus column in the 3 output prediction CSV files to indicate the consensus predictions (Consensus=1)
3. Increase the max length limitation of tRF (-n max query length ) and target (-m max target length) in RNAhybrid from 50 and 50,000 to 70 and 150,000 respectively.

Bug Fixes

1. Fix a bug of the default value for option -b or --suboptimal. Although it's said the default value is 1, but actually it's 5. Now the default value has been set to 1.

v0.1.0

The first release of tRFtarget pipeline