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- BARNA-400
fatal: early EOF fatal: index-pack failed - BARNA-397
Differential Expression on Flux capacitor output - BARNA-383
unknown macro-latex inline errors all over the place in flux simulator documentation - BARNA-381
Unable to reach the downloads for any flux package - 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-373
Capacitor does not deconvolute locus when using only sam primary alignments - BARNA-372
Output annotation mapped reads - BARNA-367
Simplification of delta values - BARNA-366
Joint deconvolution of paired-end reads - BARNA-365
Error during construction of splicing graph - BARNA-364
Flux Capacitor Tool is not found on windows - BARNA-363
qunatify gene expression of strand-specific data - BARNA-341
stabilize profiling in the presence of highly abundant transcripts added to the transcriptome annotation - BARNA-340
implement parameters for annotation sources to be included or excluded in profiling - BARNA-339
Array overflow in profiling - BARNA-338
Collapse transcripts that are exactly identical in terms of genomic coordinates of their exons - BARNA-337
Improve profiles stability - BARNA-336
SAMException - Value for tag XT is not a Character - BARNA-335
flux crashes on GTF with spike-ins - BARNA-334
Replace Attributes with Mapping properties - 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-322
Flux capacitor outputs very high incorrect RPKM values - BARNA-321
NullPointer when trying to set LP output - BARNA-318
Columns of the output gtf (quantification) file do not agree between different features - BARNA-315
Parameters for Mapping Filtering - BARNA-314
flux capacitor error:java.io.IOException: Pipe closed - BARNA-310
incorrect junction and intron coordinates - BARNA-309
Capacitor creates lots of threads when running on BAM files - BARNA-308
Capacitor does not start with single end data - BARNA-301
NullPointerException while iterating loci in BAM files - BARNA-298
Capacitor prints NaN for read count and RPKM - 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-294
Non-stranded reads erroneusly discarded? - BARNA-289
Change NO_DECOMPOSE parameter to DECONVOLUTE - BARNA-288
cannot launch Flux capacitor - BARNA-283
Add parameter to change SAM validation stringency - BARNA-275
Paired-end reads in BAM files - BARNA-273
Implement stranded annotation mapping for BAM input files - 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-266
Capacitor crashed with BED input file
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