Change log

Version notes

Dirty

• 0.16 Is now bundled with SAMtools-0.1.17 and the mpileup (and friends) command be used for passing data to dirty.
• 0.17 added extra options -minInd and -minMaf, for only printing and using sites above a threshold
• 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)
• 0.19 added support for tglf inputfiles, -tglf -posfile see runexamples, also added the likeratio test for snp calling
• 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.
• 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)
• 0.22 Well this update was a mixture of edits from user:albrecht and BGI so its difficult to give a concise description
• .0.23 Program can now read simulated files (single pop only) An example can be seen in "full example ... sfs" and input types.
• 0.24 added the tajima estimator. This should go in tandem with some R scripts. Had to modify parseargs, shared, and pml_freq_asso
• 0.25 the depth is now being populated when using mpileup -g. The program can now get the counts from mpileup

ANGSD

• 0.01.a - 0.01.b The bfgs now supports threading, maybe anders implemented a heteorzygosity estimator.
• 0.01.c A problem if we didn't observe any llh, caused the MAF estimator to 'nan'.
• 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.
• 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
• 0.3 clean version with less features. The lost features will be reintroduced later.
• 0.43 first very clean version, everything should be included
• 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
• 0.4471 error estimation is now working, the fasta reading is now threadsafe. all GLs are now likeratios.
• 0.512 After 0.500 we have changed the internal structure such that each chunk is enforced to be on the same chr. version c) fixes a problem of hardclipping
• 0.515 Alot of legacy code has been removed from mUppile.cpp. Program can now use remote files, build on code from SAMtools
• 0.520 Alot more legacy code has been removed from mUpPile.cpp. Program now does baq and adjustment of mapQ similar to -C in samtools. Also compiles on osx, but this is not supported
• 0.535 Bug in internal representation of mapQ's (only problematic for mapQ>128), we now use the flag to determine if a read has mapped. calcstat is now deprecated, users should use the bgid program now.
• 0.538 changed position output in association part. Fixed incorrect assert assumption in mUpPile.cpp. Added some downsampling options for errorEst and changed internal buffering when reading beagle files to allow for >10k individuals.
• 0.549 to many changes to remember
• 0.551 tajima paper is now published, so the emOptim2 and bgid has now been properly documented. plink output is now supported and some snp filters can be outputted.
• 0.552 minor bug when calling genotypes without defining postcutoff -> missingness couldnt occur. removed the optimSFS and emOptim from the default compilelist
• 0.553 uint removed from code.
• 0.554 plugged in sfstools functionality into main angsd, (ability to output log posts)
• 0.555 anders added some concensus stuff
• 0.556 updated the filtering (if binary rep of keep file is incomplete it is removed again. It checks timestamps to see if file has been updated), folded spectra analysis should now be working
• 0.557 There was a bug in the realsfs part of the code, that was created in the 0.556 version. 0.557 is simply a fix of this, and the removal of a warning compiler flag in the msToGlf subprogram. We only observed the problematic compiler flag on a osx machine
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