Information on coverage.  A zoomed-in IGV plot showing indels in reads.
Bigger figure for the PacBio vs. Illumina coverage plot
Finer lines for the coverage histograms
Recomputed coverage tracks with small bin size (300 vs 2500 bp)
Normalize by the median instead
Go back to normalizing by the max.  Reduce histogram line thickness.
Added GATK 3.2
A version of the 3D7 reference that has the same order as the aligned PacBio file.  The apicoplast contig has purposely been modified to be shorter than it appears in the PlasmoDB 9.0 reference.  We can get away with this because we will not be doing any analyses involving the apicoplast.
Added INDIANA jar
Control script
Ignore the cache/ directory
Show every 5000-th base in the coverage-on-ideogram plot.
Show coverage over various interesting regions
Add telomere mask inferred from absence of variant calls in the crosses
Added the telomere masking to plots
Fixed typo (hopefully) with the telomere mask
All subtelomeric repeat regions
Changed x-axis label from 'Length' to 'Position'