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| =Version notes= | | =Version notes= |
| * 0.16 Is now bundled with SAMtools-0.1.17 and the mpileup (and friends) command be used for passing data to dirty.
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| * 0.17 added extra options -minInd and -minMaf, for only printing and using sites above a threshold
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| * 0.18 added option to pass reference and ancestral allele as fasta files.(using faidx format) (doMaf is now encoded internally as a MAF_(UN)KNOWN_TYPE)
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| * 0.19 added support for tglf inputfiles, -tglf -posfile see runexamples, also added the likeratio test for snp calling
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| * 0.20 Added the check for missing data, before the major/minor. included -realSFS, changed the deallocation of the -doMAF results, such that its proper cleaned up.
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| * 0.21 refactored pml.cpp into pml_estError_genLikes.cpp and pml_freq_asso.cpp (fixed a bug that preventede -samglf and samglfclean from working)
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| * 0.22 Well this update was a mixture of edits from [[user:albrecht]] and BGI so its difficult to give a concise description
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| *.0.23 Program can now read simulated files (single pop only) An example can be seen in "full example ... sfs" and input types.
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| * 0.24 added the tajima estimator. This should go in tandem with some R scripts. Had to modify parseargs, shared, and pml_freq_asso
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| * 0.25 the depth is now being populated when using mpileup -g. The program can now get the counts from mpileup
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| ANGSD below
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| * 0.01.a - 0.01.b The bfgs now supports threading, maybe anders implemented a heteorzygosity estimator.
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| * 0.01.c A problem if we didn't observe any llh, caused the MAF estimator to 'nan'.
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| * 0.02 Fixed small bug in bfgs optimization of sfs optimization. When choosing a region bigger than what was covered by the .sfs file the program would hang. Added genotypecaller, added -sfsEst to the realSFS part of the program.
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| * 0.03 added and documented genotypecaller, can dump counts,-realSFS 1 dumps positions, -realSFS 2 is deprecated,S,pi and tajima has been added to sfstools along with possibility to do prior
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| * 0.3 clean version with less features. The lost features will be reintroduced later.
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| * 0.43 first very clean version, everything should be included
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| * 0.441 rewrote the SOAPsnp GL model, -L and -maxQ is not needed anymore. Also added an option to choose an output dir for the recalibration matrix
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| * 0.4471 error estimation is now working, the fasta reading is now threadsafe. all GLs are now likeratios.
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