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