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1.46.0 #769

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mothur-westcott opened this issue Mar 29, 2021 · 0 comments
Closed

1.46.0 #769

mothur-westcott opened this issue Mar 29, 2021 · 0 comments
Milestone
1.46.0

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@mothur-westcott
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All commits for version 1.46.0
@mothur-westcott mothur-westcott added this to the 1.46.0 milestone Mar 29, 2021
mothur-westcott added a commit that referenced this issue Mar 29, 2021
@mothur-westcott
Removes criteria parameter from cluster.fit
d558360 
#769 #415
mothur-westcott added a commit that referenced this issue Mar 29, 2021
@mothur-westcott
Adds kmer distance calc
8e9bca6 
#769 #763
mothur-westcott added a commit that referenced this issue Apr 1, 2021
@mothur-westcott
Creates function for converting string to char*
dbe9ecb 
#769
mothur-westcott added a commit that referenced this issue Apr 1, 2021
@mothur-westcott
Work on kmer dist splitting
4f71714 
#763 #769
mothur-westcott added a commit that referenced this issue Apr 2, 2021
@mothur-westcott
Update makefile
13fbcff 
#769
mothur-westcott added a commit that referenced this issue Apr 19, 2021
@mothur-westcott
Work on kmer distance split
0d32c3d 
#763 #769
mothur-westcott added a commit that referenced this issue May 8, 2021
@mothur-westcott
Work on pairwise.seqs kmer dists
8d6bfab 
#763 #769
mothur-westcott added a commit that referenced this issue May 8, 2021
@mothur-westcott
Improves cluster.split split by distance
16a4d6d 
#769
mothur-westcott added a commit that referenced this issue May 8, 2021
@mothur-westcott
Fixes bug with sra.info threads variable
a996040 
#769
mothur-westcott added a commit that referenced this issue May 8, 2021
@mothur-westcott
Adds check to shared file read for numOtus
05acf74 
#769
mothur-westcott added a commit that referenced this issue May 8, 2021
@mothur-westcott
Fixes bug with threads in sra.info
758a8e5 
#769
mothur-westcott added a commit that referenced this issue May 11, 2021
@mothur-westcott
Undo splitmatrix change
20f40be 
#769
mothur-westcott added a commit that referenced this issue May 11, 2021
@mothur-westcott
WIP kmerdist
49ee63d 
#763 #769
mothur-westcott added a commit that referenced this issue May 12, 2021
@mothur-westcott
Rework of file option rename.seqs
30f12fa 
#772 #769

The file option is now the same as the file option for make.contigs. This will allow users to rename all seqs in fastq file, removing any reads not present in all files.
mothur-westcott added a commit that referenced this issue May 12, 2021
@mothur-westcott
Removes typo space
0324ffa 
#769
mothur-westcott added a commit that referenced this issue May 21, 2021
@mothur-westcott
Adds functions to reorient and reverse unpaired primers
1f46fd5 
#769 #768
mothur-westcott added a commit that referenced this issue May 21, 2021
@mothur-westcott
Adds reorient parameter to pcr.seqs
cc67cb1 
Updates processing of trimming functions

#768 #769
mothur-westcott added a commit that referenced this issue May 21, 2021
@mothur-westcott
Updates pcr.seqs driver function
5630226 
#768 #769
mothur-westcott added a commit that referenced this issue Jun 1, 2021
@mothur-westcott
Fixes bug with OTU priority printing with file option in cluster.split
91ef82b 
#769
mothur-westcott added a commit that referenced this issue Jun 1, 2021
@mothur-westcott
Work on protein sequence class layout
937e1c1 
#776 #769
mothur-westcott added a commit that referenced this issue Jun 3, 2021
@mothur-westcott
Removes extra includes for seqDB
cba051b 
#769
mothur-westcott added a commit that referenced this issue Jun 3, 2021
@mothur-westcott
Adds ProteinDB class
bbb3164 
#769 #776

Based on the seqDB class, but handles protein sequences
mothur-westcott added a commit that referenced this issue Jun 3, 2021
@mothur-westcott
Work on protein and animo acid classes
8048ca1 
#769 #776
mothur-westcott added a commit that referenced this issue Jun 15, 2021
@mothur-westcott
Fixes segfault in metasats if abundance of one treatment is 0
ab0ed64 
#769
mothur-westcott added a commit that referenced this issue Jun 16, 2021
@mothur-westcott
WIP protdist
a25bf92 
#776 #769
mothur-westcott added a commit that referenced this issue Jun 16, 2021
@mothur-westcott
Simplifies system command in mothur
f5a9ca3 
#782 #769
mothur-westcott added a commit that referenced this issue Jun 28, 2021
@mothur-westcott
Fixes bug with get.sharedseqs shared file option
6162741 
#769
mothur-westcott added a commit that referenced this issue Jun 28, 2021
@mothur-westcott
Adds warning in remove.seqs for dereplicate
3d9053b 
#769
mothur-westcott added a commit that referenced this issue Jun 28, 2021
@mothur-westcott
Finishes jtt calculator for protein reads
a754a63 
#776 #769
mothur-westcott added a commit that referenced this issue Jul 13, 2021
@mothur-westcott
Allows unique.seqs format option to also be output
66420fa 
#769
mothur-westcott added a commit that referenced this issue Jul 14, 2021
@mothur-westcott
Minor screen output updates
89d4bb6 
#769 #778
mothur-westcott added a commit that referenced this issue Jul 14, 2021
@mothur-westcott
#769 #778
3ee5d99
mothur-westcott added a commit that referenced this issue Jul 19, 2021
@mothur-westcott
Adds common questions to chimera.uchime
9cc361a 
#769
mothur-westcott added a commit that referenced this issue Jul 19, 2021
@mothur-westcott
Updates while testing
b20e7e2 
#763 #769
mothur-westcott added a commit that referenced this issue Jul 21, 2021
@mothur-westcott
Adds kmerCutoff to pairwise.seqs fitCalc function
b1f6bbc 
#763 #769
mothur-westcott added a commit that referenced this issue Jul 23, 2021
@mothur-westcott
Removes duplicate column headers for align.report
242c888 
#785 #769
mothur-westcott added a commit that referenced this issue Jul 23, 2021
@mothur-westcott
Fixes fitCalc driver for pairwaise.seqs
930f7b0 
#769 #763
mothur-westcott added a commit that referenced this issue Jul 23, 2021
@mothur-westcott
Adds error message for missing headers
c55e885 
Prevents addition of dummy group or removal of valid group

#779 #769
mothur-westcott added a commit that referenced this issue Jul 28, 2021
@mothur-westcott
Adds kmercutoff and ksize to pairwise.seqs
d96ea8b 
#769 #763
mothur-westcott added a commit that referenced this issue Jul 29, 2021
@mothur-westcott
Adds pairwise.seqs to cluster.split for unaligned sequences
c07cfa0 
#769 #763
mothur-westcott added a commit that referenced this issue Jul 29, 2021
@mothur-westcott
Adds pairwise parameter to lefse command
dcc6b26 
#769 #781
mothur-westcott added a commit that referenced this issue Aug 3, 2021
@mothur-westcott
Updates lefse pairwise output
0b94562 
#781 #769
mothur-westcott added a commit that referenced this issue Aug 3, 2021
@mothur-westcott
WIP Adding testing batches
538f40b 
#769
mothur-westcott added a commit that referenced this issue Aug 4, 2021
@mothur-westcott
Explicitly call parent command
1e6af22 
#769
mothur-westcott added a commit that referenced this issue Aug 4, 2021
@mothur-westcott
Updates logging to accommodate set.logfile buffer
949082e 
#769
mothur-westcott added a commit that referenced this issue Aug 4, 2021
@mothur-westcott
Updates while testing
9a9d6fe 
#769
mothur-westcott added a commit that referenced this issue Aug 4, 2021
@mothur-westcott
Updates while testing
b41756a 
#769
mothur-westcott added a commit that referenced this issue Aug 4, 2021
@mothur-westcott
Updates while testing
5c74154 
#769
mothur-westcott added a commit that referenced this issue Aug 4, 2021
@mothur-westcott
Updates to cluster.split batch test
d696917 
#769
mothur-westcott added a commit that referenced this issue Aug 5, 2021
@mothur-westcott
Changes during Xcode analysis
26e7dd8 
#769
mothur-westcott added a commit that referenced this issue Aug 10, 2021
@mothur-westcott
Adds asvlist, taxonomy, count parameters
6e6a2b4 
#777 #769
mothur-westcott added a commit that referenced this issue Aug 17, 2021
@mothur-westcott
Updates make.shared from count
bbe65c8 
Modification enforces the printing of high abundance otus first

#769
mothur-westcott added a commit that referenced this issue Aug 17, 2021
@mothur-westcott
Rework of otu.hierarchy to allow for relating asv's to otus
b5e090d 
#777 #769
mothur-westcott added a commit that referenced this issue Aug 19, 2021
@mothur-westcott
Alters otuLabels to be in 3 categories
c865c00 
OtuLabel, PhlyoLabel, ASVLabel

#777 #769
mothur-westcott added a commit that referenced this issue Aug 23, 2021
@mothur-westcott
Adds howto question to otu.hierarchy
d912345 
#777 #769
mothur-westcott added a commit that referenced this issue Aug 23, 2021
@mothur-westcott
Adds batch for pairwise.seqs
a05bb93 
#769
mothur-westcott added a commit that referenced this issue Aug 23, 2021
@mothur-westcott
Adds batch test for dist.seqs
5af171b 
#769 #500
mothur-westcott added a commit that referenced this issue Aug 25, 2021
@mothur-westcott
Updates makefile version / release date
6587f73 
#769
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