move pilon out of my sandbox to gaag top-level

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@2984 333ed61c-d966-4eaf-8115-f610d1735cec
make paths relative in build script

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3027 333ed61c-d966-4eaf-8115-f610d1735cec
define "experimental" fix options; update usage string

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3028 333ed61c-d966-4eaf-8115-f610d1735cec
attempt to reduce duplicate novel sequence

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3104 333ed61c-d966-4eaf-8115-f610d1735cec
move some verbosity to debug; add OpenedGap and ClosedGap output to fixes

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3106 333ed61c-d966-4eaf-8115-f610d1735cec
don't use huge inserts (previously just warned with --debug)

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3109 333ed61c-d966-4eaf-8115-f610d1735cec
don't count Ns in +/- stats for local reassembly (break, gap filling); make assembly pruning messages under --debug

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3114 333ed61c-d966-4eaf-8115-f610d1735cec
dont use error code with no arguments...just print usage

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3198 333ed61c-d966-4eaf-8115-f610d1735cec
handle lower case bases in input genome

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3415 333ed61c-d966-4eaf-8115-f610d1735cec
handle lower case in another place

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3416 333ed61c-d966-4eaf-8115-f610d1735cec
make snp fixes much more efficient

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3420 333ed61c-d966-4eaf-8115-f610d1735cec
fix rare bounds error during indel realignment

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3429 333ed61c-d966-4eaf-8115-f610d1735cec
continuation of last fix

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3430 333ed61c-d966-4eaf-8115-f610d1735cec
clean up dead code

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3432 333ed61c-d966-4eaf-8115-f610d1735cec
debugging

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3433 333ed61c-d966-4eaf-8115-f610d1735cec
move idel relignment bounds checking earlier due to BWA alignments hanging off end of contig

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3434 333ed61c-d966-4eaf-8115-f610d1735cec
more conservative jump recruitment for gap filling

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3444 333ed61c-d966-4eaf-8115-f610d1735cec
handle lack of concensus for insertion/deletion calls better

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3446 333ed61c-d966-4eaf-8115-f610d1735cec
beginning work to identify duplication events

git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3651 333ed61c-d966-4eaf-8115-f610d1735cec
Fix off-by-1 error in start coords of pilon bed features because I
misread the spec...David Gordon pointed this out in October, but I
forgot to address it until now.



git-svn-id: https://svn.broadinstitute.org/gaag/pilon/trunk@3657 333ed61c-d966-4eaf-8115-f610d1735cec