Parameter file elements

<pedigrees>

Example	host	type	purpose
<root> .. <pedigrees> pedigrees: a,b ... </pedigrees> </root>	root	automatic-optional	hosts one to several elements each containing information about specific pedigrees

content:

• key strings

example	type	variable type	variable values	default	explanation
pedigrees: a,b	compulsory	csv word-list	pedigree names	none	list content determines nominated-compulsory elements

• nominated-compulsory elements

<jobs>

Example:

<root>
 ..
 <jobs>
  jobs: solve,yh
  ...
 </jobs>
</root>

host: root

content:

• key strings

example	type	variable type	variable values	default	explanation
jobs: solve,yh	compulsory	csv word-list	solve,sample,pevsample,mcemreml,yh	none	job sequence is determined by the list sequence. list content determines nominated-compulsory elements

• nominated-compulsory elements

<solve>

Example:

<root>
 ..
 <jobs>
  ..
  <solve>
   solver: mysolver
  </solve>
  ..
 </jobs>
 ..
</root>

host: jobs

content:

• key strings

example	type	variable type	variable values	default	explanation
solver: mysolver	compulsory	word	solver name	none	solver name must be the name of a previously defined solver

<solvers>

• host: root

<solver name>

• host: solvers
• hosts mutually exclusive elements of which hard-coded names define the solver type

<pcgiod>

• host: solver name
• defines the solver is an iteration-on-data preconditioned gradient solver

element name	element type	host element	hosts elements	element function	key string key word	key string variable	key string function	key string type
pedigrees	Automatic-optional	root	yes	host elements of specific pedigrees	pedigrees	pedigree names	nominates further elements	compulsory
pedigree name	Nominated-compulsory	pedigrees	no	host information about a specific pedigree	file	pedigree file name	provides pedigree file name	compulsory
					switch	probabilistic	pedigree is probabilistic	optional
						selfing	pedigree contains selfing
					phantomparents	integer	provides the number of individuals at the top of the pedigree which are phantom parents	optional