Merge pull request #1907 from ComparativeGenomicsToolkit/submodules

Merge pull request #1908 from ComparativeGenomicsToolkit/oneshot

fix newline bug that crashes recent tabix

quieter pecan tests

accept unchopped graphs with --vgClip et al

switch to bedtools release that has binary

update submodules and downloaded tools

Merge pull request #1906 from ComparativeGenomicsToolkit/toil-5.3

update to toil 9.3.0

Merge pull request #1901 from ComparativeGenomicsToolkit/oneshot

dont crash exporting non-existent vcf

Merge pull request #1900 from ComparativeGenomicsToolkit/ordering

Merge pull request #1899 from ComparativeGenomicsToolkit/oneshot

make sure cactus-graphmap-join uses consistent sort

add clip bypass options to rerun indexing without altering graphs