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- BARNA-376
Some boolean parameters need to be renamed to have the default value as false - BARNA-375
Add MIN_OBS parameter to allow quantifications for loci with spurious reads - BARNA-374
Capacitor overquantify a transcript in a locus when using only sam primary alignments - BARNA-370
Fragmenatation crashes with short transcripts (<4nt) - BARNA-369
Possible bug in barna.io.gtf.GTFwrapper.skipToNextChromosome() ? - BARNA-367
Simplification of delta values - BARNA-366
Joint deconvolution of paired-end reads - BARNA-336
SAMException - Value for tag XT is not a Character - BARNA-334
Replace Attributes with Mapping properties - BARNA-333
NullPointerException in BiasProfiler while iterating loci - BARNA-332
Minimum Intron Length Parameter - BARNA-331
Fragment with negative length - BARNA-330
Fraction Inconsistency - BARNA-329
AnnotationMapper maps genomic mappings spanning all-intronic edges - BARNA-328
When writing to stdout, the flux prints its version information which ends up in the GTF output - BARNA-327
Catch ParamterException in main method to hide stack trace - BARNA-326
Remove the no longer neede NR_READS_MAPPED parameter - BARNA-325
Make sort-in-ram default - BARNA-321
NullPointer when trying to set LP output - BARNA-317
Scorer cannot handle VCF files with comma-separated list in ALT field (column 5) - BARNA-315
Parameters for Mapping Filtering - BARNA-312
Event Clipper/Handler - BARNA-311
AStalavista always outputs CDS events - BARNA-309
Capacitor creates lots of threads when running on BAM files - BARNA-308
Capacitor does not start with single end data - BARNA-306
Added a seed parameter and pass it to all Random instances to make results reproducable - BARNA-305
Scorer specific parameters --vcf and --sp are not recognized - BARNA-304
Astalavista starter gives an error on startup - BARNA-303
Error while fragmenting - BARNA-297
Stats file lock might fail and then no stats are written - BARNA-296
OutOfMemoryError for some loci while getting the sorted iterator for BAM files - BARNA-289
Change NO_DECOMPOSE parameter to DECONVOLUTE - BARNA-284
JSAPResult to ParameterSchema - BARNA-283
Add parameter to change SAM validation stringency - BARNA-273
Implement stranded annotation mapping for BAM input files - BARNA-270
AStalavista option to output ALL variations of the exon-intron structure - BARNA-269
Capacitor throw NPE when trying to ouput coverage stats - BARNA-268
Capacitor throw an NPE for Ensmeble annotation - BARNA-267
The stats file writer tries to lock the stats file, but that might fail - BARNA-265
error index out of bounds fluxcapacitator - BARNA-264
Differential Expression result location misses the : between start and end - BARNA-263
BAM ID parsing error results in NPE - BARNA-261
Capacitor complains about read descriptor for bam files - BARNA-259
Add a long description to flux tools - BARNA-256
When an error occurs solving the linear system, the matrix is written on stderr and an exception is thrown even if the deconvolution continues - BARNA-253
Add Differential-Expression Tool to the Capacitor - BARNA-252
Flux launcher fails on win32 when trying to allocate more than 1.5G for JVM heap - BARNA-250
Simulator command line ignores --print-parameters - BARNA-248
Capacitor complains about READ_DESCRIPTOR when given a unindexed BAM file - BARNA-247
Capacitor still wants the -p <parameterfile> option even if I specify all mandatory paramters on the command line
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