Changed the haplotyping step so that instead of sampling the haplotype combinations for quantification the most probable combinations are selected down to a threshold (--min-hap-prob). Sampling is still employed if haplotypes are inferred independently (--ind-hap-inference) and when Gibbs sampling.
Added support for allelic mapping qualities when available in alignment file. This can be enabled using --use-allelic-mapq.
Added support for reading a gzipped haplotype/transcript info file (--path-info).
Increased the maximum fragment length threshold to better handle fragment length distributions with longer tails.
Updated the libvgio submodule version used. Please run git submodule update --init --recursive before compiling.
Changes to existing options and outputs:
Removed the option specifying for the number of haplotyping samples (--num-hap-samples). An option for setting the minimum haplotyping probability threshold was added instead (see above).
Changed Probability header name in haplotyping output to HaplotypingProbability.
Updated the Gibbs sampling option --num-gibbs-samples so that it now instead denotes the total number of Gibbs samples per transcript path. When a transcript path is not in a sampled haplotype combination a read count of zero is used.
Removed HaplotypeSampleId column from Gibbs sampling output to reduce the file size.
Bug fixes:
Fixed bug where longest alignment to a transcript path was not always used.
Improvements:
--min-hap-prob). Sampling is still employed if haplotypes are inferred independently (--ind-hap-inference) and when Gibbs sampling.--use-allelic-mapq.--path-info).Changes to existing options and outputs:
--num-hap-samples). An option for setting the minimum haplotyping probability threshold was added instead (see above).--num-gibbs-samplesso that it now instead denotes the total number of Gibbs samples per transcript path. When a transcript path is not in a sampled haplotype combination a read count of zero is used.Bug fixes: