User:Thorfinn

Thorfinns angsd todolist

0) set -outfiles=NULL in setargsstruct

0) fix return value

1) write error estimation on wiki, need more info

3. -filter to site

4. add single pars

5.

	-> angsd version: 0.567	 build(Dec  7 2013 18:15:43)
	-> No '-out' argument given, output files will be called 'angsdput'
	-> Filterfile: filt supplied will generate binary representations...
	-> Parsing chr:'1'
	-> Parsing chr:'2'
	-> Parsing chr:'3'
	-> Parsing chr:'4'
	-> Parsing chr:'5'
	-> Parsing chr:'6'
	-> Parsing chr:'7'
	-> Parsing chr:'8'
	-> Parsing chr:'9'
	-> Parsing chr:'10'
	-> Parsing chr:'11'
	-> Parsing chr:'12'
	-> Parsing chr:'13'
	-> Parsing chr:'14'
	-> Parsing chr:'15'
	-> Parsing chr:'16'
	-> Parsing chr:'17'
	-> Parsing chr:'18'
	-> Parsing chr:'19'
	-> Parsing chr:'20'
	-> Parsing chr:'21'
	-> Parsing chr:'22'
	-> Parsing chr:'X'
	-> Filtering complete: Observed: 23 different chromosomes from file:filt
	-> [analysisKeepList.cpp] Reading binary representation:filt
	-> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
Filterfile contains major/minor information
	-> [analysisKeepList.cpp] -filter is still beta, use at own risk...
Error: For sequence data (bam,SOAP) likehoods (-GL) must be specified for frequency estimation
thorfinn@pontus:~/gc_angsd$ ./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1
DEV VERSION might not work thorfinn feb 1 2013 sizeof(funkypars):128
Command:
./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1 
	-> angsd version: 0.567	 build(Dec  7 2013 18:15:43)
	-> No '-out' argument given, output files will be called 'angsdput'
	-> [analysisKeepList.cpp] Reading binary representation:filt
	-> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
Filterfile contains major/minor information