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| Thorfinns angsd todolist
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| -3) check strlen in filter -sites
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| -2) add --help and --version
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| -1) check that close gzclose on a null pointer
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| 0) set -outfiles=NULL in setargsstruct
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| 0) fix return value
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| 1) write error estimation on wiki, need more info
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| 3. -filter to site
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| 4. add single pars
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| 5.
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| <pre>
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| -> angsd version: 0.567 build(Dec 7 2013 18:15:43)
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| -> No '-out' argument given, output files will be called 'angsdput'
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| -> Filterfile: filt supplied will generate binary representations...
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| -> Parsing chr:'1'
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| -> Parsing chr:'2'
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| -> Parsing chr:'3'
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| -> Parsing chr:'4'
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| -> Parsing chr:'5'
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| -> Parsing chr:'6'
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| -> Parsing chr:'7'
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| -> Parsing chr:'8'
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| -> Parsing chr:'9'
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| -> Parsing chr:'10'
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| -> Parsing chr:'11'
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| -> Parsing chr:'12'
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| -> Parsing chr:'13'
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| -> Parsing chr:'14'
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| -> Parsing chr:'15'
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| -> Parsing chr:'16'
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| -> Parsing chr:'17'
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| -> Parsing chr:'18'
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| -> Parsing chr:'19'
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| -> Parsing chr:'20'
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| -> Parsing chr:'21'
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| -> Parsing chr:'22'
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| -> Parsing chr:'X'
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| -> Filtering complete: Observed: 23 different chromosomes from file:filt
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| -> [analysisKeepList.cpp] Reading binary representation:filt
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| -> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
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| Filterfile contains major/minor information
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| -> [analysisKeepList.cpp] -filter is still beta, use at own risk...
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| Error: For sequence data (bam,SOAP) likehoods (-GL) must be specified for frequency estimation
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| thorfinn@pontus:~/gc_angsd$ ./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1
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| DEV VERSION might not work thorfinn feb 1 2013 sizeof(funkypars):128
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| Command:
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| ./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1
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| -> angsd version: 0.567 build(Dec 7 2013 18:15:43)
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| -> No '-out' argument given, output files will be called 'angsdput'
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| -> [analysisKeepList.cpp] Reading binary representation:filt
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| -> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
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| Filterfile contains major/minor information
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| </pre>
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