Start of codon correction update#21

Open

susannah-b wants to merge 462 commits intoChrisHIV:masterfrom

susannah-b:codon_correction

This pull request is big! We're only showing the most recent 250 commits

Commits on Apr 26, 2024

Initial commit of tools/MergeAlignmentsToCsv.py

ChrisHIV
authored and
susannah-b
committed
Added references for BWA & bowtie

ChrisHIV
authored and
susannah-b
committed
Added manual

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/QuantifyPairwiseIndels.py

ChrisHIV
authored and
susannah-b
committed
Added --reference option to specify coords with respect to a named sequence.

ChrisHIV
authored and
susannah-b
committed
Updated comment

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Added comment

ChrisHIV
authored and
susannah-b
committed
Bug fix: recent change of output style from ConstructBestRef broke some other things.

ChrisHIV
authored and
susannah-b
committed
Changed progress reporting interval

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/CompareLengthsInPairwiseAln.py

ChrisHIV
authored and
susannah-b
committed
Extra options used for the published version of the paper.

ChrisHIV
authored and
susannah-b
committed
Upped the default MinGapSizeToSplitGontig from 100 to 160

ChrisHIV
authored and
susannah-b
committed
Added the option to randomly select a subset of sequences of the specified size

ChrisHIV
authored and
susannah-b
committed
Bug fix, for when two distinct parts of the same contig blast to an identical region of the same reference. (Contig pieces now have a piece number in their name.)

ChrisHIV
authored and
susannah-b
committed
More helpful error message for /1 or /2 in read names.

ChrisHIV
authored and
susannah-b
committed
Redirecting error message to stderr

ChrisHIV
authored and
susannah-b
committed
We now crash if the specified reads are not in the working dir and files with same names exist in the working directory (formerly we silently overwrote them). We now don't bother copying the reads …

ChrisHIV
authored and
susannah-b
committed
Trivial: 80 char margin rule, deleted unused code, white space.

ChrisHIV
authored and
susannah-b
committed
Initial commit of trimmomatic short cut

ChrisHIV
authored and
susannah-b
committed
Manual update

ChrisHIV
authored and
susannah-b
committed
Changed temp file names to show which is mafft --add and which is --addfragments

ChrisHIV
authored and
susannah-b
committed
Update MacInstallationNotes.txt

ChrisHIV
authored and
susannah-b
committed
Rename MacInstallationNotes.txt to InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Update InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Update InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Made FindSeqsInFasta take either names or a file of names as an optional arg; changed the bash appropriately; made the bash report a helpful error message if all contigs fail the length threshold.

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/AddAllPossibleSNPsToSeqs.py

ChrisHIV
authored and
susannah-b
committed
Keep all original seq names in the output (not using a mutated name where one mutated seq matches another original seq).

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/ExactBLAST.py

ChrisHIV
authored and
susannah-b
committed
Added option to trim primers containing a single SNP (turned off by default) instead of just exact matches.

ChrisHIV
authored and
susannah-b
committed
Added two new read pairs for testing primer trimming.

ChrisHIV
authored and
susannah-b
committed
Bug fix: from Feb 2nd 2018 till now, removal of contaminant reads before mapping will have failed. This probably had very little effect on the mapped reads with default settings, because each read …

ChrisHIV
authored and
susannah-b
committed
Set default TrimPrimerWithOneSNP=false

ChrisHIV
authored and
susannah-b
committed
The pairwise alignment for HXB2 coords now uses linsi be default rather than mafft.

ChrisHIV
authored and
susannah-b
committed
Changed the criterion for selecting between mafft --addfragments or --add: now it's minimum alignment length. The old method is now an option (not the default one).

ChrisHIV
authored and
susannah-b
committed
Bug fix: the user supplying the mapping reference HXB2, named exactly as shiver's copy, previously broke the part where we align to HXB2 and compare names.

ChrisHIV
authored and
susannah-b
committed
shiver_align_contigs.sh now returns an exit status of 2 if and only if (the contig file is empty OR no contigs are long enough OR no contigs have a blast hit to the existing references.

ChrisHIV
authored and
susannah-b
committed
Changed 'no HIV contigs' exit code from 2 to 3, as 2 has a special meaning generally in bash.

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/EstimateAmbiguousBases.py

ChrisHIV
authored and
susannah-b
committed
Added count information where ambiguous bases were interpreted.

ChrisHIV
authored and
susannah-b
committed
Added --keep-gaps-by-missing and --use-n-for-missing options

ChrisHIV
authored and
susannah-b
committed
Added CallAmbigBaseIfNeeded func

ChrisHIV
authored and
susannah-b
committed
Added --skip-ref-in-output option

ChrisHIV
authored and
susannah-b
committed
Bug fix: now returns exit status 3 instead of 1 if no good HIV contigs were found, as previously intended.

ChrisHIV
authored and
susannah-b
committed
Return an exit status of 3 if no reads mapped.

ChrisHIV
authored and
susannah-b
committed
Now return an exit status of 3 if there are no reads initally, after trimming, or after cleaning.

ChrisHIV
authored and
susannah-b
committed
Added --ignore-n option

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/CleanGlobalAln.py

ChrisHIV
authored and
susannah-b
committed
Removed unused code

ChrisHIV
authored and
susannah-b
committed
Removed hard-coded skipping of BEE0006-2

ChrisHIV
authored and
susannah-b
committed
Added comments

ChrisHIV
authored and
susannah-b
committed
When splitting up into separate alignments for each region, made the exclusion of patients with too high missingness match that used earlier (max 20%).

ChrisHIV
authored and
susannah-b
committed
Initial commit of info/ToDoListForImprovingShiver.txt

ChrisHIV
authored and
susannah-b
committed
By default we now prepend temp_ to the pre-mapping read filenames; this can be changed in config.sh

ChrisHIV
authored and
susannah-b
committed
Changed the suffix for the reads after cleaning from 'clean' to 'PreMapping', to reflect that more cleaning may be needed.

ChrisHIV
authored and
susannah-b
committed
Made the file of contigs passing the length threshold temporary.

ChrisHIV
authored and
susannah-b
committed
Exit with status 3 instead of 1 if splitting the aligned corrected contigs at overly large gaps then imposing the second length threshold results in no contigs.

ChrisHIV
authored and
susannah-b
committed
Added --trim-missing-ends option

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Updated my email address

ChrisHIV
authored and
susannah-b
committed
Email address typo

ChrisHIV
authored and
susannah-b
committed
Restructuring ahead of option for individual consensuses: seqs now read in after all blacklists, and we no longer check blacklists for patients we don't have.

ChrisHIV
authored and
susannah-b
committed
Moved private TranslateSeqCoordsToAlnCoords function to ShiverFuncs

ChrisHIV
authored and
susannah-b
committed
Rewrite of tools/CleanGlobalAln.py to allow individual consensus files as input.

ChrisHIV
authored and
susannah-b
committed
File renamed

ChrisHIV
authored and
susannah-b
committed
Made the --split-amplicons option provide the usual output as well.

ChrisHIV
authored and
susannah-b
committed
Changed output files to be labelled by seq id instead of beehive id

ChrisHIV
authored and
susannah-b
committed
Bug fix: individual consensuses files that only became wholly undetermined after blacklisting were output. Now they aren't. Also wholly undetermined checks now check for a single determined base in…

ChrisHIV
authored and
susannah-b
committed
Added --skip-string option

ChrisHIV
authored and
susannah-b
committed
bug fix - missing arg namespace

ChrisHIV
authored and
susannah-b
committed
Added --undetermined-start and --undetermined-end options

ChrisHIV
authored and
susannah-b
committed
Added --longest-gap option

ChrisHIV
authored and
susannah-b
committed
Made multiple input fasta files possible

ChrisHIV
authored and
susannah-b
committed
Added --first-seq-only option

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/AlignBaseFreqFiles_ByConsensuses.py

ChrisHIV
authored and
susannah-b
committed
File renamed

ChrisHIV
authored and
susannah-b
committed
Discussion of the AlignBaseFreqFiles differences

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Updated to-do list

ChrisHIV
authored and
susannah-b
committed
Updated diagram

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/CallGlobalConsensusFromCsv.py

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Critical bug fix for Mac OS - it's sort --merge --unique command seems to silently fail, producing no output and causing shiver's contaminant read removal to silently fail. Replaced that command wi…

ChrisHIV
authored and
susannah-b
committed
Added check that the length of the most common kmer is the most common kmer length, warning if not.

ChrisHIV
authored and
susannah-b
committed
smalt brew command updated

ChrisHIV
authored and
susannah-b
committed
mafft now installable from brew

ChrisHIV
authored and
susannah-b
committed
Removed superfluous reordering of blast hits from testing

ChrisHIV
authored and
susannah-b
committed
Moved RemoveBlankColumns function into ShiverFuncs. Defined GetSeqStartAndEndPos there too.

ChrisHIV
authored and
susannah-b
committed
Added --trim-overhangs option to CutAlignedContigs, and made it remove pure-gap columns.

ChrisHIV
authored and
susannah-b
committed
Made it the default to trim contigs that overhang the edge of the alignment of references.

ChrisHIV
authored and
susannah-b
committed
Renamed tools/SplitGappyContigs.py to tools/CutAlignedContigs.py

ChrisHIV
authored and
susannah-b
committed
Clarified message

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Bug fix: the AlignContigsToConsensus option gave an error due to an old variable name problem.

ChrisHIV
authored and
susannah-b
committed
Added --header option to tools/KeepBestLinesInDataFile.py

ChrisHIV
authored and
susannah-b
committed
In tools/KeepBestLinesInDataFile.py, exit(1) if no data found.

ChrisHIV
authored and
susannah-b
committed
Fix for bug from minutes ago: tested emptiness of wrong object.

ChrisHIV
authored and
susannah-b
committed
Updated comment

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Trivial bug fix for newer Biopython that doesn't allow comparison of a seq object to None

ChrisHIV
authored and
susannah-b
committed
Made output arg compulsory. Changed expected header of seq-based blacklist.

ChrisHIV
authored and
susannah-b
committed
More generic shebang

ChrisHIV
authored and
susannah-b
committed
Added option to clean base freq files

ChrisHIV
authored and
susannah-b
committed
Now add to our blacklist those seqs that were skipped because they were wholly undetermined after removing all lower-case bases.

ChrisHIV
authored and
susannah-b
committed
Removed print hangover from testing

ChrisHIV
authored and
susannah-b
committed
Changed default behaviour to be masking any bases before the first or after the last amplicon. Can be undone with the --keep_overhangs option.

ChrisHIV
authored and
susannah-b
committed
Trivial fix of recent bug that would have stopped the individual consensus option from working at all.

ChrisHIV
authored and
susannah-b
committed
For the split_amplicons output for individual consensuses, leading and trailing runs of N are now trimmed.

ChrisHIV
authored and
susannah-b
committed
Moved post-mapping steps into the function ProcessBam. Trivial bug fix: if the reference file contained more than one sequence, I didn't catch this error till later than intended.

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/process_bam.sh

ChrisHIV
authored and
susannah-b
committed
Trivial movement of variable assignment to avoid repetition

ChrisHIV
authored and
susannah-b
committed
Minor bug fix for tools/CleanConsensuses.py: now masks anything before the first region and after the last region as intended.

ChrisHIV
authored and
susannah-b
committed
Trivial bug fix: one occurence of samtools instead of meant it would not have worked if samtools were not in your $PATH.

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/GetCoverageFromBamFile.py

ChrisHIV
authored and
susannah-b
committed
samtools BAQ calculation now turned off by deafult, as seems to be appropriate for HIV, c.f. https://tinyurl.com/noBAQnoCry

ChrisHIV
authored and
susannah-b
committed
Bug fix / improvement: previously contigs that were discarded for being too short were treated as contaminants for the read cleaning step (discarding those reads that blast best to discarded contig…

ChrisHIV
authored and
susannah-b
committed
Updated shiver diagram

ChrisHIV
authored and
susannah-b
committed
Added --dont_blacklist_missingness to tools/CleanConsensuses.py

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/RecoverAlteredUpperLowerCase.py

ChrisHIV
authored and
susannah-b
committed
Allow full control of which blast options are used for the contigs (no change to default behaviour).

ChrisHIV
authored and
susannah-b
committed
tools/CorrectContigs.py: added option to output remaining blast hits

ChrisHIV
authored and
susannah-b
committed
tools/CorrectContigs.py: don't bother converting evalue and pident from strings to floats, since we don't use them, and better to not modify for the blast output option (it's then easier to do a di…

ChrisHIV
authored and
susannah-b
committed
Gave tools/CorrectContigs.py the compulsory option OverlapFracToMerge

ChrisHIV
authored and
susannah-b
committed
Added the flexibility to try multiple different blast task modes when blasting contigs, and merge results where hits strongly (or at least partially) overlap. The defaults are set such that this do…

ChrisHIV
authored and
susannah-b
committed
Clarified comment

ChrisHIV
authored and
susannah-b
committed
Improvement for rare edge case in tools/EstimateAmbiguousBases.py: if a base cannot be estimated, use N instead of quitting.

ChrisHIV
authored and
susannah-b
committed
Deleting shiver_reprocess_bam.sh because it's superseded by tools/process_bam.sh

ChrisHIV
authored and
susannah-b
committed
Minor bug fix for a crash caused by a very large number of contaminant contigs

ChrisHIV
authored and
susannah-b
committed
Trivial fix: redirecting an error message from stdout to stderr

ChrisHIV
authored and
susannah-b
committed
Clarified error message if a position after the end of the reference was encountered. Clarified help.

ChrisHIV
authored and
susannah-b
committed
Added file name safety check to tools/TranslateSeqForGlobalAln.py to avoid use on remapped consensuses.

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Changed tools/GetCoverageFromBamFile.py to output reference positions as 1-based instead of 0-based, for compatibility with other output.

ChrisHIV
authored and
susannah-b
committed
Minor bug fix: now when cleaning the reads, if none of the forward or none of the reverse reads blast at all, instead of crashing we proceed to mapping (which will likely map none of the read pairs).

ChrisHIV
authored and
susannah-b
committed
Redirected an error message from stdout to stderr

ChrisHIV
authored and
susannah-b
committed
Minor bugfix: if there was precisely 1 pair of reads blasting better to the contaminant congtigs than the reference, these were not discarded before mapping due to a line break issue. (With more th…

ChrisHIV
authored and
susannah-b
committed
We no longer sort reads as a prelude to read cleaning. This is more robust to pairing errors when 'sort' produces different results on forward and reverse reads (thanks to Gu-Lung Lin for pointing …

ChrisHIV
authored and
susannah-b
committed
Minor bugfix resulting from recent change, where precisely zero contaminant reads caused a crash.

ChrisHIV
authored and
susannah-b
committed
Added a contaminant read pair to the example data that trigger cleaning.

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Added --allow-duplicates option to tools/FindSeqsInFasta.py

ChrisHIV
authored and
susannah-b
committed
Print how the script was called, and what the config file parameter values were.

ChrisHIV
authored and
susannah-b
committed
Added clarifying comment

ChrisHIV
authored and
susannah-b
committed
In tools/LinkIdentityToCoverage.py, changed the default behaviour to be ignoring sequence in an overlap between reads in a pair, the second time it is encountered. Also it now skips unmapped reads …

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/LinkIdentityToCoverage_CombineBams.py

ChrisHIV
authored and
susannah-b
committed
In tools/CleanConsensuses.py, made the patient_based_blacklist argument a csv file instead of a plain text file for ease of including comments in it

ChrisHIV
authored and
susannah-b
committed
Added script explanatory message

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/CleanConsensusesOxford.py

ChrisHIV
authored and
susannah-b
committed
In tools/CleanConsensusesNoAmplicons.py, made the dates input file optional.

ChrisHIV
authored and
susannah-b
committed
Call all python scripts with user-specified python exectuable.

ChrisHIV
authored and
susannah-b
committed
Update InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Update InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Update InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Update InstallationNotes.sh

ChrisHIV
authored and
susannah-b
committed
Minor bug fix: the optional description field on fastq identifier lines was causing FindNamedReadsInSortedFastq.py to crash.

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Updated funcs.sh and map_reads.sh
susannah-b
committed
Modified config and FindContaminantReadPairs to allow unpaired
susannah-b
committed
FindContaminantReadPairs.py bash script for unpaired data, plus fixes
susannah-b
committed
Further edits across map_reads and funcs to correctly handle unpaired data
susannah-b
committed
Added a check for /1 or /2 suffixes in the unpaired data CheckReadNames function
susannah-b
committed
Renamed unpaired reads variable, moved some checks, restructured section on finding contaminants, removed CheckFilesExist_Unpaired

S Blundell
authored and
susannah-b
committed
Consolidated unpaired/paired functions, moved trimmomatic sanity checks, and other fixes

S Blundell
authored and
susannah-b
committed
Some fatal bugs fixed; others remain

ChrisHIV
authored and
susannah-b
committed
sam_to_bam bug fixed

ChrisHIV
authored and
susannah-b
committed
Testing done - minor edits made to CheckConfig
susannah-b
committed
More informative error messages for bad config file options for unpaired read data

ChrisHIV
authored and
susannah-b
committed
Checks for samtools -f flag values incompatible with unpaired data

S Blundell
authored and
susannah-b
committed
More informative error messages for samtoolsReadFlags

ChrisHIV
authored and
susannah-b
committed
Used CheckForPaired instead of Paired inside CheckConfig for consistency/robustness. Bug fix for unpaired data with MapContaminantReads=true. Restored default config trimmomatic value. Insert size …

ChrisHIV
authored and
susannah-b
committed
Moved code that was present in both 'if paired' and 'if unpaired' outside of the if/else scope. Simplified string comparison of the Paired variable to use of its necessarily boolean/logical value.

ChrisHIV
authored and
susannah-b
committed
Trivial bug fix: don't create the MappedContaminantReads file if the user has said not to and there are no reads to map

ChrisHIV
authored and
susannah-b
committed
Updated manual re: paired/unpaired

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Codon correction update for shiver, including standalone CodonCorrectionInit.sh and CodonCorrection.sh scripts, as well as a reference file of annotatable genomes, and a file of gene positions for …

S Blundell
authored and
susannah-b
committed
Improved handling of sequences with missing coverage

S Blundell
authored and
susannah-b
committed
Improve handling of arguments and errors. Separated gene extraction python code to a separate script. Added a check for failed alignments.
susannah-b
committed
Corrected indel detection, added a check for single sequences in the corrected file, and checks sequence length
susannah-b
committed
Added call_virulign function to simplify code. Added a function to append additional bases (N) to the end of the reference in cases where virulign truncates the sample due to a shorter reference.
susannah-b
committed
Added colours to more easily identify warnings/errors
susannah-b
committed
Removed debug failed directory as the alignments that failed did not enter and the ones that seem successful did - replaced with custom error handling. Only add genes to frameshift.txt if not fail…
susannah-b
committed
Modified init script to instead create a BLASTn database per gene, and created a python function script to later consolidate all python code
susannah-b
committed
Replaced the whole-genome approach with BLAST-ing to individual genes instead, allowing the reference to be tailored to the gene. Also migrated the python code over to Python_Funcs.py so all python…
susannah-b
committed
Added frameshift positional information, improved python error handling, customised gap penalty settings, added handling of pre-existing N bases, and other small structural changes
susannah-b
committed
Updated for Python 3
susannah-b
committed
Fixed grep issue when MissingCoverage.txt does not exist.

S Blundell
authored and
susannah-b
committed
Only Python2-style print

ChrisHIV
authored and
susannah-b
committed
from __future__ needed for previous print change

ChrisHIV
authored and
susannah-b
committed
modernize itertools_six

ChrisHIV
authored and
susannah-b
committed
modernize map

ChrisHIV
authored and
susannah-b
committed
modernize xrange_six

ChrisHIV
authored and
susannah-b
committed
modernize dict_six

ChrisHIV
authored and
susannah-b
committed
modernize classic_division

ChrisHIV
authored and
susannah-b
committed
2to3 manual correction of modernize classic_division

ChrisHIV
authored and
susannah-b
committed
modernize idioms

ChrisHIV
authored and
susannah-b
committed
Prepended '_' to all internal variable names for comprehensions to be defensive against Python 2 memory leak

ChrisHIV
authored and
susannah-b
committed
Changed Biopython's deprecated ungap() for replace()

ChrisHIV
authored and
susannah-b
committed
Extra(previously missed) change of Biopython's deprecated ungap() for replace()

ChrisHIV
authored and
susannah-b
committed
Try both .ungap() and .replace() on seq objects for flexibility with Biopython versions

ChrisHIV
authored and
susannah-b
committed
Replaced fastaq conversion from fastq to fasta with own code

ChrisHIV
authored and
susannah-b
committed
Changed reference construction to break ties between which contig to use (when they have equal length) and which existing reference to use (when they have equal fractional similarity to the flatten…

ChrisHIV
authored and
susannah-b
committed
Changed default python from 2 to 3. Renamed python2 variable to python.

ChrisHIV
authored and
susannah-b
committed
Fixed bug affecting only temp file temp_GappyRefWithExtraSeq.fasta: the elongated existing reference used to fill in gaps beween contigs, shown only for comparison, had the first line of sequence m…

ChrisHIV
authored and
susannah-b
committed
renamed variable for clarity

ChrisHIV
authored and
susannah-b
committed
Moved imports to the top. Enforced importation from a given module on exactly one line.

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Changed ContigMinBlastOverlapToMerge in config to switch on some merging of overlapping blast hits, following overwhelmingly postitive testing of performance. Added testing features to tools/Correc…

ChrisHIV
authored and
susannah-b
committed
Added --help and --test options to the main three bash scripts

ChrisHIV
authored and
susannah-b
committed
Added to all executable Python scripts if __name__ == "__main__":

ChrisHIV
authored and
susannah-b
committed
Initial commit of tools/TestPythonModulesInstalled.py

ChrisHIV
authored and
susannah-b
committed
Changed python2 shebangs to python

ChrisHIV
authored and
susannah-b
committed
Removed unnecessary import

ChrisHIV
authored and
susannah-b
committed
Removed tools/trimmomatic and instead added instructions how to make this (if needed) to config.sh, to avoid this taking precedence over the more robust trimmomatic binary in conda shiver

ChrisHIV
authored and
susannah-b
committed
Deleted example contigs for full auto mode

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Updated manual

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Update README.md

ChrisHIV
authored and
susannah-b
committed
Adjusted file locations to align with new shiver structure.
susannah-b
committed
Adjusted file structure for /shiver/bin
susannah-b
committed
Implemented the ungap auxiliary function for biopython version compatibility
susannah-b
committed
Basic shiver implementation WIP - currently returns an Init Directory error
susannah-b
committed

Commits on May 1, 2024

Commits on May 3, 2024