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Add draft of clustering functionality; restructure directory layout to be inline with nimble recommendations; add .nimble file #1

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merged 14 commits into from
Nov 21, 2020
Merged

Add draft of clustering functionality; restructure directory layout to be inline with nimble recommendations; add .nimble file #1

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68f06e8
first commit for clustering branch
Oct 25, 2020
3697d13
get junctions from BAM CIGAR
Oct 26, 2020
e83cde1
basic options parsing, beginning debug
Nov 11, 2020
72d1e8b
Populating clustering graph
Nov 13, 2020
c06a6c7
Adding kde calculation for determining splice sites locations
Nov 14, 2020
ee1c398
Adding outputting of clusters in FASTA format
Nov 15, 2020
2ce8106
removing a bunch of dead / commented code blocks, beginning the proce…
Nov 19, 2020
83f9a93
more moving code around, cleaning up dead code, etc
Nov 19, 2020
ecd14fa
Adding proc for correcting alignments based on the corresponding refe…
Nov 19, 2020
ee6b2bc
code style cleanup, etc
Nov 20, 2020
51a1df1
linking threadpools
Nov 20, 2020
6616821
Restructuring code directories to conform to nimble standard, adding …
Nov 20, 2020
c9e7bf3
more code restructuring
Nov 21, 2020
a0296eb
Adding warning about conduit clustering
Nov 21, 2020
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5 changes: 4 additions & 1 deletion .gitignore
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Expand Up @@ -5,19 +5,22 @@
!*/

# Whitelist gitignore, scripts, and figures
!.gitmodules
!.gitignore
!CONDUIT.png
!**.py
!**.R
!**.bsh
!**.nim
!**.nims
!**.nimble
!**.md
!**.c
!**.h
!**.rst
!**.html
!Makefile
!poaV2/Makefile
!LICENSE
!poaV2/Makefile
!poaV2/LICENSE
!poaV2/myNUC3.4.4.mat
3 changes: 3 additions & 0 deletions .gitmodules
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@@ -0,0 +1,3 @@
[submodule "threadpools"]
path = src/threadpools
url = https://github.com/yglukhov/threadpools.git
7 changes: 4 additions & 3 deletions Makefile
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@@ -1,7 +1,8 @@
NIM = nim c

conduit:
cd poaV2 && make
$(NIM) -d:release --threads:on --passL:poaV2/liblpo.a --passL:poaV2/align_score.o conduit.nim
$(NIM) -d:release conduitUtils.nim
cd src/poaV2 && make
mkdir bin/
cd src/ && $(NIM) -d:release --threads:on --passL:poaV2/liblpo.a --passL:poaV2/align_score.o conduit.nim && mv src/conduit bin/
cd src/ && $(NIM) -d:release conduitUtils.nim && mv src/conduitUtils bin/

19 changes: 19 additions & 0 deletions conduit.nimble
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@@ -0,0 +1,19 @@
# Package

version = "0.1.0"
author = "Nathan Roach"
description = "De novo transcriptome assembler"
license = "GPLv2"

# Dependencies

requires "hts >= 0.3.1", "nim >= 1.0.0"

srcDir = "src/"

before install:
echo "Building poaV2"
withDir "src/poaV2":
exec "make"

bin = @["conduit", "conduitUtils", "conduit_clustering"]
311 changes: 15 additions & 296 deletions conduit.nim → src/conduit.nim
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3 changes: 3 additions & 0 deletions src/conduit.nims
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switch("threads", "on")
switch("passL","src/poaV2/liblpo.a")
switch("passL","src/poaV2/align_score.o")
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