Assemble command trackback & confidence values >=1

[qoiopipq]

Previously I posted to this thread #7, because some of the polyA events have confidence values >=1.

My very first attempt was to run assemble command without specifying '-c' parameter. It went well but I got 3827/8921 polyA events with confidence values >=1 from the following compare command. Then I set '-c' parameter to zero in assemble step (got this hint from thread #7 ), but I got this following trackback:
2016-01-27T14:20:48,581 [main] INFO executable.IsoSCM - Starting assemble ...
2016-01-27T14:20:49,465 [main] INFO executable.IsoSCM - tabulating splice junctions...
2016-01-27T14:21:51,295 [main] INFO executable.IsoSCM - counting junction supporting reads...
2016-01-27T14:31:14,485 [main] INFO executable.IsoSCM - identifying covered segments...
2016-01-27T14:48:21,038 [main] INFO executable.IsoSCM - merging coverage gaps less than 100 bp...
2016-01-27T14:48:28,718 [main] INFO executable.IsoSCM - filtering splice junctions...
2016-01-27T14:48:33,916 [main] INFO executable.IsoSCM - identifying spliced exons...
2016-01-27T14:48:37,654 [main] INFO executable.IsoSCM - identifying change points...
Exception in thread "main" java.lang.IllegalArgumentException: fromIndex(15) > toIndex(14)
at java.util.ArrayList.subListRangeCheck(ArrayList.java:1006)
at java.util.ArrayList.subList(ArrayList.java:996)
at scm.ConfidenceCalculator.calculateConfidence(ConfidenceCalculator.java:31)
at scm.IdentifyChangePoints.identifyConstrainedNegativeBinomialPoints(IdentifyChangePoints.java:245)
at scm.IdentifyChangePoints.identifyNegativeBinomialChangePointsInLongSegments(IdentifyChangePoints.java:660)
at executable.IsoSCM.main(IsoSCM.java:358)

I ran assemble command with and without '-c' parameter on the same bam file. Here is the bam file that caused the problem in assemble step with '-c' parameter(https://drive.google.com/file/d/0B1phbPEoxK3zTDZWT0d3U2s4SlU/view?usp=sharing)

Any feedback on how to solve the problem is welcome.

[shenkers]

Thank you for sharing the file that was causing the problem. I was able to reproduce this error for the file you shared when the '-c' parameter is set to '0'. This problem is corrected this in version 2.0.12 (available at https://github.com/shenkers/isoscm/releases/tag/IsoSCM-2.0.12 ). In version 2.0.12 the -c parameter is no longer available, and is always set to 0. Consequently, the confidence values will always be reported in the correct range (between 0-1.0) when using the new version.

Thanks for reporting this, and please don't hesitate to ask if you run into any more problems.