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- 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-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 - BARNA-246
UnixSorter line interceptor called for each merge step instead of just the final one - BARNA-242
When counting Splice Junctions and Introns, output the correct GeneID of a locus if multiple Genes are contained - BARNA-240
Capacitor runs out of Heap Space with some BAM files - BARNA-239
Parameter Schema relative path parser extends Windows paths - BARNA-238
Wrong number of reads detected in some BAM input files - BARNA-235
Flux-simulator does not accept SIZE_DISTRIBUTION N(300,30) - BARNA-233
JSAPResult workaround for using command line arguments as a alternative to parameter files - BARNA-230
Astalavista command line options are printed twice, unter tool options and under general options - BARNA-229
Capacitor throws a NullPointer exception on a BAM file - BARNA-227
Implement Site Scoring - BARNA-219
Error while generating reads from a one-transcript gene - BARNA-215
Sequencing fails with ArrayIndexOutOfBoundsException - BARNA-196
Error: SIZE_DISTRIBUTION with N(mean, sd) won't work. It just doesn't. - BARNA-187
Make mated Flux Simulator IDs equal - BARNA-186
Update BED wrapper for CASAVA 1.8 read descriptor - BARNA-184
Mutated characters should be lower case - BARNA-76
Refactor Astalavista
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