09-30-2013: More robust and faster LSC 0.3.1
09-30-2013: More robust and faster LSC 0.3.1
In LSC 0.3.1, we don't have pseudo chromosome, the alignment time reduced to ~10% (in Bowtie2 mode). And you can re-run some crashed jobs easily now.
New features:
Remove pseudo-chr processing
Accept compressed SR as input (should be named SR.fa.cps/SR.fa.cps.idx in any folder)
Added "runLSC -cleanup" option to remove redundant files (per thread split, remaining _tmp files) if the run was successful at the end.
Changed convertNav to sort reads and then generate LR_SR.map (memory optimization instead of loading all alignments in memory)
Miscellaneous changes:
Changed "print" to system.echo (messages were not printed out in qsub output files)
Changed a little bit "cleanup" option to keep per thread data (*.aa, *.ab, ..). It was useful when one thread was crashed and we wanted to just re-run that at the end
Any feedback or bug report is very welcomed! Please contact [email protected]
In LSC 0.3.1, we don't have pseudo chromosome, the alignment time reduced to ~10% (in Bowtie2 mode). And you can re-run some crashed jobs easily now.
New features:
Remove pseudo-chr processing
Accept compressed SR as input (should be named SR.fa.cps/SR.fa.cps.idx in any folder)
Added "runLSC -cleanup" option to remove redundant files (per thread split, remaining _tmp files) if the run was successful at the end.
Changed convertNav to sort reads and then generate LR_SR.map (memory optimization instead of loading all alignments in memory)
Miscellaneous changes:
Changed "print" to system.echo (messages were not printed out in qsub output files)
Changed a little bit "cleanup" option to keep per thread data (*.aa, *.ab, ..). It was useful when one thread was crashed and we wanted to just re-run that at the end
Any feedback or bug report is very welcomed! Please contact [email protected]