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1.47.0 #792

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mothur-westcott opened this issue Sep 14, 2021 · 0 comments
Closed

1.47.0 #792

mothur-westcott opened this issue Sep 14, 2021 · 0 comments
Milestone
Version 1.42.0

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@mothur-westcott
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@mothur-westcott mothur-westcott added this to the Version 1.42.0 milestone Sep 14, 2021
mothur-westcott added a commit that referenced this issue Sep 14, 2021
@mothur-westcott
Removes deprecated include
579cfd3 
#792
mothur-westcott added a commit that referenced this issue Sep 14, 2021
@mothur-westcott
Fixes bug with get.sharedseqs if no groups are provided
681a952 
#792
mothur-westcott added a commit that referenced this issue Sep 14, 2021
@mothur-westcott
Minor modifications
467e798 
#792
mothur-westcott added a commit that referenced this issue Sep 17, 2021
@mothur-westcott
Minor changes
5ac44ae 
#792
mothur-westcott added a commit that referenced this issue Sep 21, 2021
@mothur-westcott
Fixes bug with remove.groups phylip file option
5d74e8e 
#792
mothur-westcott added a commit that referenced this issue Sep 21, 2021
@mothur-westcott
Forces pairwise comparison with 2 treatments in lefse
78156ea 
#792
mothur-westcott added a commit that referenced this issue Sep 21, 2021
@mothur-westcott
Removes auto check for name file
07b5cde 
#792
mothur-westcott added a commit that referenced this issue Sep 22, 2021
@mothur-westcott
Sets default output for unique.seqs to count
d1d3574 
#792
mothur-westcott added a commit that referenced this issue Sep 22, 2021
@mothur-westcott
Changes make.contigs output from group to count
ca27345 
#793 #792
mothur-westcott added a commit that referenced this issue Sep 24, 2021
@mothur-westcott
Adds maxambig, maxhomop, maxlength parameters to make.contigs
55a2211 
#792 #793
mothur-westcott added a commit that referenced this issue Sep 24, 2021
@mothur-westcott
Fixes formatting issue with chimera.vsearch with a reference
024400e 
#792
mothur-westcott added a commit that referenced this issue Oct 5, 2021
@mothur-westcott
Adds list to output types get.seqs internal
f597278 
#792
mothur-westcott added a commit that referenced this issue Oct 5, 2021
@mothur-westcott
Adds sorting to pcr.seqs to force order
60cc15c 
#792
mothur-westcott added a commit that referenced this issue Oct 6, 2021
@mothur-westcott
Fixes bug in sens.spec when name file is used
3c49bd8 
#792
mothur-westcott added a commit that referenced this issue Oct 12, 2021
@mothur-westcott
Fixes crash with sort.seqs if multiple seqs present with the same name
291cfd1 
#792
mothur-westcott added a commit that referenced this issue Oct 12, 2021
@mothur-westcott
MOTHUR_FILES can now contain multiple paths separated by ';'
bd1a590 
#792 #799
mothur-westcott added a commit that referenced this issue Oct 13, 2021
@mothur-westcott
Adds mothurhome keyword
66e0455 
#800 #792
mothur-westcott added a commit that referenced this issue Oct 19, 2021
@mothur-westcott
Updates MOTHUR_TOOLS to allow for multiple locations
4edc9e8 
#792 #799
mothur-westcott added a commit that referenced this issue Oct 19, 2021
@mothur-westcott
Removes preserve order in pcr.seqs
efae207 
#792 #797
mothur-westcott added a commit that referenced this issue Oct 20, 2021
@mothur-westcott
Allows for multiple input directories
91b2fff 
#792 #799
mothur-westcott added a commit that referenced this issue Oct 25, 2021
@mothur-westcott
Adds removechimeras parameter to chimera.vsearch
30da436 
Default=t, meaning auto remove chimeras found in input files.

#795 #792
mothur-westcott added a commit that referenced this issue Oct 25, 2021
@mothur-westcott
Removes sort option from pcr.seqs
51da4d5 
#792
mothur-westcott added a commit that referenced this issue Oct 25, 2021
@mothur-westcott
Removes dereplicate warning from remove.seqs
04f8f37 
Default change to remove chimeras automatically eliminates the need for this

#792
mothur-westcott added a commit that referenced this issue Oct 27, 2021
@mothur-westcott
Adds removechimeras parameter to chimera.uchime
0968fd9 
#795 #792

Default=t
mothur-westcott added a commit that referenced this issue Oct 27, 2021
@mothur-westcott
Minor mods
0906b7f 
#792 #795
mothur-westcott added a commit that referenced this issue Oct 27, 2021
@mothur-westcott
Adds removechimeras parameter to chimera.slayer
9c085f2 
#792 #795

Default=t
mothur-westcott added a commit that referenced this issue Oct 27, 2021
@mothur-westcott
Adds removechimeras parameter to chimera.pintail
3448aa7 
#792 #795

Default=t
mothur-westcott added a commit that referenced this issue Oct 28, 2021
@mothur-westcott
Adds removechimeras to chimera.perseus
cee65a2 
#792 #795
mothur-westcott added a commit that referenced this issue Oct 28, 2021
@mothur-westcott
Adds removechimeras to chimera.ccode
e206fe8 
#792 #795
mothur-westcott added a commit that referenced this issue Nov 16, 2021
@mothur-westcott
Removes amino acid to dna code
02a4cce 
#788 #792
mothur-westcott added a commit that referenced this issue Nov 30, 2021
@mothur-westcott
Minor modifications to output filenames
9c9987e 
#792
mothur-westcott added a commit that referenced this issue Nov 30, 2021
@mothur-westcott
Adds ability to input multiple files
919d88f 
Will help with file mismatch issues

#792 #803
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Updates Ubuntu build instructions
f8fa3f6 
#792
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Adds multiple files option to the remove.seqs command
ad75ceb 
Aids in fixing file mismatches in paired files

#792 #803
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Removes BLAST data structure files
cf42d13 
#792 #801
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Removes search and blastlocation parameters from chimera.slayer
005caf5 
#792 #801
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Removes blast as a search option from classify.seqs
b640cec 
#792 #801
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Removes blast as option from align.seqs
7cfb3f4 
#792 #801
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Removes blastlocation parameter from set.dir
fbbd0b6 
#792 #801
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Removes blast as search option in pairwise.seqs
b1bc90b 
#792 #801
mothur-westcott added a commit that referenced this issue Dec 1, 2021
@mothur-westcott
Removes blast as option for search in pre.cluster
7324187 
#792 #801
mothur-westcott added a commit that referenced this issue Dec 3, 2021
@mothur-westcott
Adds validFastqGZFiles function
603f4be 
#804 #792
mothur-westcott added a commit that referenced this issue Dec 3, 2021
@mothur-westcott
Adds ability to read compressed fastq files in list.seqs
479813d 
#804 #792
mothur-westcott added a commit that referenced this issue Dec 13, 2021
@mothur-westcott
Fixed bug that caused logger to segfault
d8d2ecb 
#792
mothur-westcott added a commit that referenced this issue Dec 13, 2021
@mothur-westcott
Fixes maxint declaration
56f86ca 
#792
mothur-westcott added a commit that referenced this issue Dec 14, 2021
@mothur-westcott
WIP
07713e0 
#792 #804
mothur-westcott added a commit that referenced this issue Dec 14, 2021
@mothur-westcott
Adds ability to write compressed files in get.seqs
457517b 
#792 #804
mothur-westcott added a commit that referenced this issue Dec 14, 2021
@mothur-westcott
Adds trimming to translate.seqs
6abd4db 
#788 #792
mothur-westcott added a commit that referenced this issue Jan 3, 2022
@mothur-westcott
Updates to unique.seqs
31f557a 
Includes filename changes from deconvolute to unique.seqs

#792 #807
mothur-westcott added a commit that referenced this issue Jan 4, 2022
@mothur-westcott
Fixes read of singleton file in cluster.split
79902c0 
Caused by the change to sparse count table by default

#792
mothur-westcott added a commit that referenced this issue Jan 7, 2022
@mothur-westcott
Adds internal constructor for remove.seqs
189cc2c 
#792
mothur-westcott added a commit that referenced this issue Jan 7, 2022
@mothur-westcott
Adds ability to read name file into count table
666d3b5 
Removes the warning about removing groups

#792
mothur-westcott added a commit that referenced this issue Jan 7, 2022
@mothur-westcott
Trim.seqs now outputs a count file instead of a name or group file
bfc2071 
Fixes small bugs in trim.seqs found while testing

#792
mothur-westcott added a commit that referenced this issue Jan 10, 2022
@mothur-westcott
Fixes trim.seqs bug if nothing is scrapped
c2633a6 
#792
mothur-westcott added a commit that referenced this issue Jan 10, 2022
@mothur-westcott
Adds timing output for the shhh.flows command
521571b 
#792
mothur-westcott added a commit that referenced this issue Jan 14, 2022
@mothur-westcott
Updates to release info
865be67 
#792
mothur-westcott added a commit that referenced this issue Jan 20, 2022
@mothur-westcott
Fixes while testing
d443289 
#792
mothur-westcott added a commit that referenced this issue Jan 20, 2022
@mothur-westcott
Fixes bug while testing
349d95f 
#792
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