-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathVERSION
64 lines (63 loc) · 3.27 KB
/
VERSION
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
0.9.1
version 0.9.1
Fixed a bug in abundances when primers were not used ('-') and adding in new metadata (including -S to abundances).
version 0.9.0
New functions: preprocess step can analyze reads with inline barcodes (where the barcode sequence was attached to primers used in the initial PCR reaction), single barcoded reads can be processed. The classify app can filter by length (minL parameter) when no minQ parameter is set, and also works on joined reads.
version 0.8.7
Worked on a few issues as well as added capability to flip
version 0.8.6
change RDP classify to use allrank instead of fixrank, only when using a custom db (WARNING: Db must only use major ranks, eg class,family,genus,species)
version 0.8.5
added the ability to use an environmental variable for the path to the RDP classifier, using the env variable RDP_PATH
version 0.8.4
changed default behavior of abudances to output abundance/proportion tables every time and the --biom flag ALSO produces a biom file, so no need to run abundances twice anymore to produce tables and biom.
version 0.8.3
changed versionReport.sh to dbcVersionReport.sh also added new parameters to preprocessing add to rc (or not) Index 1, and Index 2, also changed all references in barcodes P5/P7 to I1 and I2, some simplicity
version 0.8.2.1
Added small shell script in scripts/ to generate version numbers for entire pipeline
version 0.8.2
Added new subscript preprocPair_with_inlineBC.py to convert 2 read inline barcode exp to the four read type needed for dbcAmplicons
version 0.8.1
Numerous bug/issue fixes, fix bug in screen, added code to check version and prompt for update when github is newer
version 0.8.0
Merged in deduplication code, fixed error in c primer alignment of last 4 bases added --test to classify
version 0.7.0
Reworked all the barcode and primer to be faster, implementation of deduplication code
version 0.6.6
Added support for variable length barcodes in convert2ReadTo4Read.py
version 0.6.5
Show error message and download for RDP when not found
version 0.6.4
modified abundance output, flash output and reporting, fix issue #12
version 0.6.3
addressed issue #11, validate pairs in primer file
version 0.6.2
bugfixes and cleanup, merge customRDP, scripts, mapping with develop, close issue #1, varius bug fixes
version 0.6.1
added validate app, some pep modification and various tweeks
version 0.6.0
added support for output of biom format in abundance tables
version 0.5.9
added script to split by sample, appending output files through iterations
version 0.5.8
fixed bug in barcodes mismatches, added two new flags to preprocess keep primer and test
version 0.5.7
increased speed in gzip read, and bug fixes
version 0.5.6
added support for Fluidgm down stream processing of samples, in scripts/R
version 0.5.5
added support for gzip in a separate process and ability to infer read file names
version 0.5.4
added convert2ReadTo4Read.py script in scripts folder, minor edits to main dbcAmplicons application
version 0.5.3
added support for project with no primers
version 0.5.2
rdp classification and abundance table generation available
version 0.5.1
added support for rdp classification
version 0.5.0
reconfigure repository and interface
version 0.4.0
add support for multiple input files
version 0.3.0
initial release add support for preprocess and splitreads