remove erroneous error when bed end coordinate is equal to sequence length.
fix indento
Revert "fix indento"

This reverts commit 720ca26b7a1522f6a018ea7af58b0e972b54e6cf.
fix indento
change sed option order to work on mac too
try changing each maf to ss before affregating
fix sonlib build dependency
add noAncestors option
fix other indent error i think
quick hack to try splitting bed files
add slicesize option for hal2maf
fix weird disappearing character
disable maxbedlines by default now that msa_view seems to be working
disable writing empty sequences in wiggle
disable conversion of maf to ss before aggregation
add --tree option to override the tree in the hal file
remove hack to take dots out of sequence names
try to fix a few bugs in the segment traversal
add chromSizes option to halStats for use with wigToBigWig
add complement flag to halAlignedExtract to get out insertions wrt parent