Minor bugfixes and updates

Updates

• Additional mitochondrial modifications from Clark 2016 added to additionalMods.txt
• GSNAP index names match input files not experiment name flag
• DESeq2 threshold for significance now adjusted p < 0.01
• readthroughTable proportion now 1 - stop proportion at position, reflecting actual readthrough
• DESeq2 single replicates now get normalised count outputs using estimateSizeFactors()

Bugfixes

• Strict handling of additionalMods location type (i.e. mito or cytosolic) when adding to modified position index
• Correct handling of insertions between cluster parent and child: modified sites after insertions in child need position correction by number of insertions (i.e. all mods after insertions are decreased to adjust for parent insertions)
• Indel handling for discrepancy between GSNAP an usearch. In some cases the two algorithms chose different, closely spaced positions to introduce an insertion, effecting downstream cluster splitting and mod position analysis
• Fixed isodecoders added to unique_isodecoderMMs based on insertions that weren't unique to one isodecoder only
• Adjust position of mismatch between parent and child if there are preceding insertions so that the correct position in the child is used for storing the identity of the mismatch