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Implemented --genomeSuffixLengthMax option to control max suffix length at the genome generation step.
Fixed a bug that caused genome generation stalling in some cases.
In Aligned.toTranscriptome.out.bam (--quantMode TranscriptomeSAM), non-primary SAM flag is assigned to all but one randomly selected alignment in Aligned.toTranscriptome.out.bam .
Fixed a bug that filtered out some chimeric junctions.
Fixed a bug that prevented chimeric output for some of the "circular" configurations.
