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CHANGELOG
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CHANGELOG
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v1.14:
-Fixed some genes being annotated with end position shifted -1.
-Fixed error with miraMapping module when having non paired-end libraries.
-Fixed: MIRA would throw an error when using more than 7 libraries in mapping assembly.
v1.13.7:
-Fixed error when annotating duplicated regions with chloroplast_Maker.py
-Fixed tRNAs found in the complementary strand not being marked as so.
-Changed: stop codon won't be counted for the translated sequence anymore.
v1.13.6:
-Fixed annotations in genbank file being 1 base forward for certain tRNAs.
v1.13.5
-Added: sanity check for when an assembler encounters an error, but a best build was found.
v1.13.4:
-Fixed some tRNAs being warned as not found, when they were actually found and annotated.
v.1.13.3:
-Fixed: error being thrown when only one contig was enough to finish the assembly!
-Fixed: some errors when deleting temporary files if not using a reference.
v1.13.2:
-Added sanity check to keep the program running even if MITObim didn't run, but MIRA mapping did.
v1.13.1:
-Fixed SPAdes not running sometimes with paired-end libraries.
v1.13:
-Improved logs from recursiveSPAdes and recursiveMira.
-Recompiled binaries for SPAdes.
-Fixed: recursiveSPAdes not considering the -p flag.
-Fixed some instances of the actual best build not being selected.
v1.12:
-Logs of recursiveSOAP.py should now be more informative in case of problems.
v1.11:
-Added --keepfolders to keep temporary folders created during a mitoMaker software run.
By default, these folders are cleaned up once the program is finished.
-Improved various warning and error messages in terms of readability and specifications.
v1.1:
-Added support to SPAdes genome assembler. In order to use it in the De-Novo step, use --spades flag.
v1.03:
-Organized and commented a few more parts of the code.
-Added a new metric when selecting the best build (validContigs). If an assembly has the same number of features found and
hasn't circularized, the program will pick the one that has the least amount of contigs used to form it. After that it picks the
sequence length without counting N's.
v1.02:
-Changed default final results to file to be the ordered (starting at tRNA-Phe) result.
-Unordered result now has termination .unordered.
-If a tRNA is found containing an intron, a warning will be raised to the user and on the .stats file.
-Added cleanup of various temporary files.
-Fixed: some rRNAs being translated.
v1.01:
-Updated SOAPdenovo-Trans to 1.04 (from 1.03)
v1.0:
-Changed: MIRA will not stop running when in a NFS mounted drive.
WARNING: running MIRA ina NFS drive can cause severe slowdowns.
v1.0rc6:
-Added: option to run with SOAPdenovo instead of SOAP-Trans.
By default mitoMaker and cloroplastMaker will run with SOAP-Trans.
v1.0rc5:
-Fixed problem with naming tRNAs when annotating.
-Changed: increased font size of PNG annotation image.
v1.0rc4:
-Fixed tRNAscan-SE not searching with correct genetic code, when one different from vertebrate mitochondria was given.
v1.0rc3:
-Fixed small bug when inputting start and end positions found with tRNAscan-SE on tRNAs that were found with blastn.
v1.0rc2:
-Small changes to the .png annotation visualization file (color schemes mainly)
v1.0rc1:
-Created new branch called generalMaker: split into 3 files -> mitoMaker.py, cloroplastMaker.py and generalMaker.py
generalMaker is the main script for handling the assemblies, you can call it as you called plastidMaker.py
mitoMaker will call generalMaker with the flags you specify and more specific ones to mitochondrial DNA
cloroplastMaker will call generalMaker with the flags you specify and more specific ones to cloroplast DNA (BETA)
-Added: .png annotation result that shows each feature relative position in a png image file