git.donarmstrong.com Git - mothur.git/commit

]> git.donarmstrong.com Git - mothur.git/commit

author	Sarah Westcott <mothur.westcott@gmail.com>
	Thu, 13 Dec 2012 21:33:31 +0000 (16:33 -0500)
committer	Sarah Westcott <mothur.westcott@gmail.com>
	Thu, 13 Dec 2012 21:33:31 +0000 (16:33 -0500)
commit	1a5c2356c1b955c6ec024b2baf9f46377ee7c72e
tree	71debc8d05114b98c33fda9ed41188eb8d404351	tree \| snapshot
parent	79a7d3273749b08d4f9f8dfe350c964ff0c4351e	commit \| diff

fixed bug in phylo.diversity rooting. added filename patterns and create filename methods to all commands.

259 files changed:

aligncommand.cpp		diff \| blob \| history
aligncommand.h		diff \| blob \| history
amovacommand.cpp		diff \| blob \| history
amovacommand.h		diff \| blob \| history
anosimcommand.cpp		diff \| blob \| history
anosimcommand.h		diff \| blob \| history
binsequencecommand.cpp		diff \| blob \| history
binsequencecommand.h		diff \| blob \| history
catchallcommand.cpp		diff \| blob \| history
catchallcommand.h		diff \| blob \| history
chimerabellerophoncommand.cpp		diff \| blob \| history
chimerabellerophoncommand.h		diff \| blob \| history
chimeraccodecommand.cpp		diff \| blob \| history
chimeraccodecommand.h		diff \| blob \| history
chimeracheckcommand.cpp		diff \| blob \| history
chimeracheckcommand.h		diff \| blob \| history
chimeraperseuscommand.cpp		diff \| blob \| history
chimeraperseuscommand.h		diff \| blob \| history
chimerapintailcommand.cpp		diff \| blob \| history
chimerapintailcommand.h		diff \| blob \| history
chimeraslayercommand.cpp		diff \| blob \| history
chimeraslayercommand.h		diff \| blob \| history
chimerauchimecommand.cpp		diff \| blob \| history
chimerauchimecommand.h		diff \| blob \| history
chopseqscommand.cpp		diff \| blob \| history
chopseqscommand.h		diff \| blob \| history
classifyotucommand.cpp		diff \| blob \| history
classifyotucommand.h		diff \| blob \| history
classifyseqscommand.cpp		diff \| blob \| history
classifyseqscommand.h		diff \| blob \| history
classifysharedcommand.cpp		diff \| blob \| history
classifysharedcommand.h		diff \| blob \| history
classifytreecommand.cpp		diff \| blob \| history
classifytreecommand.h		diff \| blob \| history
clearcutcommand.cpp		diff \| blob \| history
clearcutcommand.h		diff \| blob \| history
clearmemorycommand.cpp		diff \| blob \| history
clearmemorycommand.h		diff \| blob \| history
clustercommand.cpp		diff \| blob \| history
clustercommand.h		diff \| blob \| history
clusterdoturcommand.cpp		diff \| blob \| history
clusterdoturcommand.h		diff \| blob \| history
clusterfragmentscommand.cpp		diff \| blob \| history
clusterfragmentscommand.h		diff \| blob \| history
clustersplitcommand.cpp		diff \| blob \| history
clustersplitcommand.h		diff \| blob \| history
collectcommand.cpp		diff \| blob \| history
collectcommand.h		diff \| blob \| history
collectsharedcommand.cpp		diff \| blob \| history
collectsharedcommand.h		diff \| blob \| history
command.hpp		diff \| blob \| history
commandparameter.h		diff \| blob \| history
consensusseqscommand.cpp		diff \| blob \| history
consensusseqscommand.h		diff \| blob \| history
cooccurrencecommand.cpp		diff \| blob \| history
cooccurrencecommand.h		diff \| blob \| history
corraxescommand.cpp		diff \| blob \| history
corraxescommand.h		diff \| blob \| history
countgroupscommand.cpp		diff \| blob \| history
countgroupscommand.h		diff \| blob \| history
countseqscommand.cpp		diff \| blob \| history
countseqscommand.h		diff \| blob \| history
createdatabasecommand.cpp		diff \| blob \| history
createdatabasecommand.h		diff \| blob \| history
deconvolutecommand.cpp		diff \| blob \| history
deconvolutecommand.h		diff \| blob \| history
degapseqscommand.cpp		diff \| blob \| history
degapseqscommand.h		diff \| blob \| history
deuniqueseqscommand.cpp		diff \| blob \| history
deuniqueseqscommand.h		diff \| blob \| history
deuniquetreecommand.cpp		diff \| blob \| history
deuniquetreecommand.h		diff \| blob \| history
distancecommand.cpp		diff \| blob \| history
distancecommand.h		diff \| blob \| history
filterseqscommand.cpp		diff \| blob \| history
filterseqscommand.h		diff \| blob \| history
getcommandinfocommand.cpp		diff \| blob \| history
getcommandinfocommand.h		diff \| blob \| history
getcoremicrobiomecommand.cpp		diff \| blob \| history
getcoremicrobiomecommand.h		diff \| blob \| history
getcurrentcommand.cpp		diff \| blob \| history
getcurrentcommand.h		diff \| blob \| history
getgroupcommand.cpp		diff \| blob \| history
getgroupcommand.h		diff \| blob \| history
getgroupscommand.cpp		diff \| blob \| history
getgroupscommand.h		diff \| blob \| history
getlabelcommand.cpp		diff \| blob \| history
getlabelcommand.h		diff \| blob \| history
getlineagecommand.cpp		diff \| blob \| history
getlineagecommand.h		diff \| blob \| history
getlistcountcommand.cpp		diff \| blob \| history
getlistcountcommand.h		diff \| blob \| history
getotulabelscommand.cpp		diff \| blob \| history
getotulabelscommand.h		diff \| blob \| history
getoturepcommand.cpp		diff \| blob \| history
getoturepcommand.h		diff \| blob \| history
getotuscommand.cpp		diff \| blob \| history
getotuscommand.h		diff \| blob \| history
getrabundcommand.cpp		diff \| blob \| history
getrabundcommand.h		diff \| blob \| history
getrelabundcommand.cpp		diff \| blob \| history
getrelabundcommand.h		diff \| blob \| history
getsabundcommand.cpp		diff \| blob \| history
getsabundcommand.h		diff \| blob \| history
getseqscommand.cpp		diff \| blob \| history
getseqscommand.h		diff \| blob \| history
getsharedotucommand.cpp		diff \| blob \| history
getsharedotucommand.h		diff \| blob \| history
hclustercommand.cpp		diff \| blob \| history
hclustercommand.h		diff \| blob \| history
heatmapcommand.cpp		diff \| blob \| history
heatmapcommand.h		diff \| blob \| history
heatmapsimcommand.cpp		diff \| blob \| history
heatmapsimcommand.h		diff \| blob \| history
helpcommand.h		diff \| blob \| history
homovacommand.cpp		diff \| blob \| history
homovacommand.h		diff \| blob \| history
indicatorcommand.cpp		diff \| blob \| history
indicatorcommand.h		diff \| blob \| history
libshuffcommand.cpp		diff \| blob \| history
libshuffcommand.h		diff \| blob \| history
listotulabelscommand.cpp		diff \| blob \| history
listotulabelscommand.h		diff \| blob \| history
listseqscommand.cpp		diff \| blob \| history
listseqscommand.h		diff \| blob \| history
loadlogfilecommand.cpp		diff \| blob \| history
loadlogfilecommand.h		diff \| blob \| history
makebiomcommand.cpp		diff \| blob \| history
makebiomcommand.h		diff \| blob \| history
makecontigscommand.cpp		diff \| blob \| history
makecontigscommand.h		diff \| blob \| history
makefastqcommand.cpp		diff \| blob \| history
makefastqcommand.h		diff \| blob \| history
makegroupcommand.cpp		diff \| blob \| history
makegroupcommand.h		diff \| blob \| history
mantelcommand.cpp		diff \| blob \| history
mantelcommand.h		diff \| blob \| history
matrixoutputcommand.cpp		diff \| blob \| history
matrixoutputcommand.h		diff \| blob \| history
mergefilecommand.cpp		diff \| blob \| history
mergefilecommand.h		diff \| blob \| history
mergegroupscommand.cpp		diff \| blob \| history
mergegroupscommand.h		diff \| blob \| history
metastatscommand.cpp		diff \| blob \| history
metastatscommand.h		diff \| blob \| history
mgclustercommand.cpp		diff \| blob \| history
mgclustercommand.h		diff \| blob \| history
newcommandtemplate.cpp		diff \| blob \| history
newcommandtemplate.h		diff \| blob \| history
nmdscommand.cpp		diff \| blob \| history
nmdscommand.h		diff \| blob \| history
nocommands.h		diff \| blob \| history
normalizesharedcommand.cpp		diff \| blob \| history
normalizesharedcommand.h		diff \| blob \| history
otuassociationcommand.cpp		diff \| blob \| history
otuassociationcommand.h		diff \| blob \| history
otuhierarchycommand.cpp		diff \| blob \| history
otuhierarchycommand.h		diff \| blob \| history
pairwiseseqscommand.cpp		diff \| blob \| history
pairwiseseqscommand.h		diff \| blob \| history
parsefastaqcommand.cpp		diff \| blob \| history
parsefastaqcommand.h		diff \| blob \| history
parselistscommand.cpp		diff \| blob \| history
parselistscommand.h		diff \| blob \| history
parsimonycommand.cpp		diff \| blob \| history
parsimonycommand.h		diff \| blob \| history
pcacommand.cpp		diff \| blob \| history
pcacommand.h		diff \| blob \| history
pcoacommand.cpp		diff \| blob \| history
pcoacommand.h		diff \| blob \| history
pcrseqscommand.h		diff \| blob \| history
phylodiversitycommand.cpp		diff \| blob \| history
phylodiversitycommand.h		diff \| blob \| history
phylotypecommand.cpp		diff \| blob \| history
phylotypecommand.h		diff \| blob \| history
pipelinepdscommand.cpp		diff \| blob \| history
pipelinepdscommand.h		diff \| blob \| history
prcseqscommand.cpp		diff \| blob \| history
preclustercommand.cpp		diff \| blob \| history
preclustercommand.h		diff \| blob \| history
quitcommand.h		diff \| blob \| history
rarefactcommand.cpp		diff \| blob \| history
rarefactcommand.h		diff \| blob \| history
rarefactsharedcommand.cpp		diff \| blob \| history
rarefactsharedcommand.h		diff \| blob \| history
readtree.cpp		diff \| blob \| history
removegroupscommand.cpp		diff \| blob \| history
removegroupscommand.h		diff \| blob \| history
removelineagecommand.cpp		diff \| blob \| history
removelineagecommand.h		diff \| blob \| history
removeotulabelscommand.cpp		diff \| blob \| history
removeotulabelscommand.h		diff \| blob \| history
removeotuscommand.cpp		diff \| blob \| history
removeotuscommand.h		diff \| blob \| history
removerarecommand.cpp		diff \| blob \| history
removerarecommand.h		diff \| blob \| history
removeseqscommand.cpp		diff \| blob \| history
removeseqscommand.h		diff \| blob \| history
reversecommand.cpp		diff \| blob \| history
reversecommand.h		diff \| blob \| history
screenseqscommand.cpp		diff \| blob \| history
screenseqscommand.h		diff \| blob \| history
secondarystructurecommand.cpp		diff \| blob \| history
secondarystructurecommand.h		diff \| blob \| history
sensspeccommand.cpp		diff \| blob \| history
sensspeccommand.h		diff \| blob \| history
seqerrorcommand.cpp		diff \| blob \| history
seqerrorcommand.h		diff \| blob \| history
seqsummarycommand.cpp		diff \| blob \| history
seqsummarycommand.h		diff \| blob \| history
setcurrentcommand.cpp		diff \| blob \| history
setcurrentcommand.h		diff \| blob \| history
setdircommand.cpp		diff \| blob \| history
setdircommand.h		diff \| blob \| history
setlogfilecommand.cpp		diff \| blob \| history
setlogfilecommand.h		diff \| blob \| history
sffinfocommand.cpp		diff \| blob \| history
sffinfocommand.h		diff \| blob \| history
sffmultiplecommand.cpp		diff \| blob \| history
sffmultiplecommand.h		diff \| blob \| history
sharedcommand.cpp		diff \| blob \| history
sharedcommand.h		diff \| blob \| history
shhhercommand.cpp		diff \| blob \| history
shhhercommand.h		diff \| blob \| history
shhhseqscommand.cpp		diff \| blob \| history
shhhseqscommand.h		diff \| blob \| history
sortseqscommand.cpp		diff \| blob \| history
sortseqscommand.h		diff \| blob \| history
splitabundcommand.cpp		diff \| blob \| history
splitabundcommand.h		diff \| blob \| history
splitgroupscommand.cpp		diff \| blob \| history
splitgroupscommand.h		diff \| blob \| history
splitmatrix.cpp		diff \| blob \| history
subsample.cpp		diff \| blob \| history
subsamplecommand.cpp		diff \| blob \| history
subsamplecommand.h		diff \| blob \| history
summarycommand.cpp		diff \| blob \| history
summarycommand.h		diff \| blob \| history
summaryqualcommand.cpp		diff \| blob \| history
summaryqualcommand.h		diff \| blob \| history
summarysharedcommand.cpp		diff \| blob \| history
summarysharedcommand.h		diff \| blob \| history
summarytaxcommand.cpp		diff \| blob \| history
summarytaxcommand.h		diff \| blob \| history
systemcommand.cpp		diff \| blob \| history
systemcommand.h		diff \| blob \| history
tree.cpp		diff \| blob \| history
treegroupscommand.cpp		diff \| blob \| history
treegroupscommand.h		diff \| blob \| history
trimflowscommand.cpp		diff \| blob \| history
trimflowscommand.h		diff \| blob \| history
trimseqscommand.cpp		diff \| blob \| history
trimseqscommand.h		diff \| blob \| history
unifracunweightedcommand.cpp		diff \| blob \| history
unifracunweightedcommand.h		diff \| blob \| history
unifracweightedcommand.cpp		diff \| blob \| history
unifracweightedcommand.h		diff \| blob \| history
venncommand.cpp		diff \| blob \| history
venncommand.h		diff \| blob \| history

Mothur--16S microbiota sequencing software; mirror of main repository with my branches

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