Details
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Bug
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Status: Resolved
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Major
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Resolution: Fixed
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Capacitor 1.3 (API 1.23), Capacitor 1.4 (API 1.24)
Description
Hi
When running flux-capacitor 1.3 or 1.4 I am getting these exceptions(it works with 1.2.4):
[PROFILE] Scanning the input and getting the attributes.
profiling [ERROR] Error while iterating loci:
net.sf.samtools.SAMException: Value for tag XT is not a Character: class java.lang.String
at net.sf.samtools.SAMRecord.getCharacterAttribute(SAMRecord.java:975)
at barna.model.sam.SAMMapping.<init>(SAMMapping.java:51)
at barna.model.sam.SAMMapping.<init>(SAMMapping.java:60)
at barna.io.sam.SAMMappingIterator.init(SAMMappingIterator.java:86)
at barna.io.sam.SAMMappingIterator.<init>(SAMMappingIterator.java:70)
at barna.io.sam.SAMReader.read(SAMReader.java:227)
at barna.flux.capacitor.profile.BiasProfiler.profile(BiasProfiler.java:205)
at barna.flux.capacitor.profile.BiasProfiler.call(BiasProfiler.java:101)
at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2196)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1878)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
at barna.commons.launcher.Flux.main(Flux.java:197)
I have attatched the log file. The files I am using for the quantification can be accessed from here if needed:
BAM:
http://genome.crg.es/~pprieto/flux-bug/0780N0013_AGTCAA_L001_r12.Ggal71.gsnap0819.sorted.bam
Gtf:
http://genome.crg.es/~pprieto/flux-bug/pc_only.gtf