HMM-Flagger v1.1.0

Changes since v1.0.0:

• Tuned HMM-Flagger for different platforms
• Updated mobinasri/long_read_aligner:v1.1.0 with minimap2-2.28
• Added minHighMapqRatio parameter for restricting transition to collapsed state (with the default value of 0.75)
• Reduced the default value of mapqThreshold to 10 for bam2cov program
• Added a WDL parameter for decomposing censat bed file. With this option censat annotation bed file that is created with centromereAnnotation.wdl can be passed directly to HMM-Flagger WDLs.
• Added --writePosteriorProbs option (for development purposes)
• Added --startOnly mode to consider only the start locations of reads for computing coverage (experimental)