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pull main codebase #1

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merged 108 commits into from
Sep 25, 2021
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32f5643
developing
nchernia Aug 17, 2017
f0317a2
mostly working version of 1.6
nchernia Aug 25, 2017
4096a0a
fixed small bug in chimeric script, added alignonly mode to juicer
nchernia Aug 25, 2017
ca2f9ad
working out kinks with mapq0 shunting and BWA versions and flags
nchernia Sep 12, 2017
b3aaa05
further bug fixes to encode pipeline
nchernia Nov 7, 2017
b5c0939
added in differing collisions treatment, taking out collisions script
nchernia Nov 7, 2017
497f26b
adding bam to text script, adjusting stats
nchernia Nov 8, 2017
7095d6f
adding bam to text script
nchernia Nov 8, 2017
a093190
fix bug with call to bwa
nchernia Nov 8, 2017
ec0a6fe
Update juicer.sh
theaidenlab Nov 15, 2017
099b50a
Update juicer.sh
theaidenlab Nov 15, 2017
063d046
Update juicer.sh
theaidenlab Nov 15, 2017
2582632
Update juicer.sh
theaidenlab Nov 15, 2017
7ff22d9
adding in no check when not needed for different stages
nchernia Nov 15, 2017
38330c6
fixed bug
nchernia Nov 15, 2017
1da25fb
updating to include option for flags -1 and -2 to read in files from …
nchernia Jan 25, 2018
5b5bd5e
Bug fix for postproc stage; bug fix for when count ligations takes lo…
nchernia Apr 6, 2018
95c361d
Update generate_site_positions.py
SooLee May 3, 2018
9c55ecb
Merge pull request #61 from SooLee/patch-1
nchernia May 3, 2018
f44753e
change to call alignonly without chrom.sizes; merging moved to approp…
nchernia May 17, 2018
5dd887a
A complete rewrite of generate_site_positions.py
ecsedi Nov 3, 2018
124cbd5
Update calculate_map_resolution.sh
jemilianosf Jan 7, 2019
84f6957
Merge pull request #92 from jemilianosf/patch-1
nchernia Jan 7, 2019
7b8a26b
multithreading for "bwa aln"
Zojka Jan 30, 2019
23f80dd
Moved Library Complexity into jar
nchernia Feb 1, 2019
43cc35f
Merge pull request #96 from Zojka/Zojka-patch-1
nchernia Feb 1, 2019
2817f1a
Make executable
sidiropoulos Feb 25, 2019
06475c3
Set delimiter to nothing when pasting fastq files
sidiropoulos Feb 25, 2019
6b6a074
Indent lines after if-else statements
sidiropoulos Feb 25, 2019
cebaffc
Add juicer_tools script
sidiropoulos Feb 25, 2019
da5002c
Make executable
sidiropoulos Feb 25, 2019
4851e36
Tidy code
sidiropoulos Feb 25, 2019
1cc6c95
Tidy code
sidiropoulos Feb 25, 2019
ba6d69d
Account for gzipped fastq files
sidiropoulos Feb 25, 2019
968032d
Merge branch 'master' of https://github.com/aidenlab/juicer into PBS_fix
sidiropoulos Feb 25, 2019
00bb6c2
Merge pull request #97 from sidiropoulos/PBS_fix
nchernia Feb 25, 2019
957de09
adding in addstats script for mega
nchernia Feb 25, 2019
2ea1ae1
updating to modern version of mega.sh; adding the sum awk script for …
nchernia Feb 25, 2019
284cb33
CPU additions for justexact option, no fragment maps by default, chan…
nchernia Apr 6, 2019
518c0a1
merging changes from master
nchernia Apr 6, 2019
d3039d4
handles multiple ligation junctions
nchernia Apr 18, 2019
4f6480a
updated makemega addstats to go with latest stats;
nchernia Apr 18, 2019
08ba135
added ligation option
nchernia Apr 18, 2019
94ec691
fixed some small issues that might have resulted in script reporting …
nchernia Apr 25, 2019
e8b29eb
fixed some small issues that might have resulted in script reporting …
nchernia Apr 25, 2019
53fe7de
Merge branch 'encode' of https://github.com/aidenlab/juicer into encode
nchernia Apr 25, 2019
6be7c0f
updating names to be consistent with new jar
nchernia Apr 26, 2019
4475223
Merge pull request #112 from aidenlab/master
sa501428 May 21, 2019
8283bab
adding user flag #106
nchernia May 23, 2019
94e871e
chimeric script should ignore header lines in SAM files
nchernia Jun 4, 2019
9e2b476
some systems do not have zcat. also grep now handles more complicated…
nchernia Jun 4, 2019
f9e9bd8
adding in capability of no wobble / just exact duplicates
nchernia Jun 4, 2019
b18e0fb
Major changes:
nchernia Jun 4, 2019
a52e176
Making scripts more consistent by having check for system for juicer_…
nchernia Jun 4, 2019
809943d
minor update to mem request
nchernia Jun 4, 2019
90e05b2
Adding in options to mega script; updating memory requirements
nchernia Jun 4, 2019
92de655
Adding in flag for no wobble / just exact duplicates
nchernia Jun 4, 2019
d696dd1
adding ability to handle multiple ligation junctions
nchernia Jun 4, 2019
91dbb87
Merged changes from master
nchernia Jun 4, 2019
26f20f3
rollback encode changes in add user branch
nchernia Jun 5, 2019
17957c5
rollback
nchernia Jun 5, 2019
59f69c2
Merge pull request #117 from aidenlab/add_user
nchernia Jun 5, 2019
c563d66
Create CODE_OF_CONDUCT.md
nchernia Aug 1, 2019
8879636
Update issue templates
sa501428 Aug 1, 2019
93a262f
Create CONTRIBUTING.md
sa501428 Aug 1, 2019
7bba4c5
Update CONTRIBUTING.md
nchernia Aug 1, 2019
503d032
Update CODE_OF_CONDUCT.md
nchernia Aug 1, 2019
097b690
Update CONTRIBUTING.md
sa501428 Aug 1, 2019
da4bfd0
One should set memory before calling juicer_tools; e.g. via export _J…
nchernia Aug 8, 2019
cf8f91e
Some cleanup with Voltron-specific options; added back in the -l flag…
nchernia Aug 8, 2019
a3a239a
Adding ligation junction option #122, adding scripts option #124. Mak…
nchernia Aug 8, 2019
3bc6889
Merge branch 'master' of https://github.com/theaidenlab/juicer
nchernia Aug 8, 2019
2d89085
We have merged LibraryComplexity into parent jar and now recommend ex…
nchernia Aug 8, 2019
39ceb9f
adjusting the ordering of the stats jobs to be correct; eliminating t…
nchernia Aug 8, 2019
217a5e5
changing email address
nchernia Aug 8, 2019
74a70ed
Got rid of LibraryComplexity class; moved statistics into things that…
nchernia Aug 8, 2019
beaa79e
deleting separate LibraryComplexity class
nchernia Aug 8, 2019
8891985
Adding options for ligation junction and setting scripts directory; f…
nchernia Aug 8, 2019
bc2c911
Quote ligation regex
cErikson Aug 8, 2019
72de043
Add Arima Ligation
cErikson Aug 8, 2019
fd76062
Added ligation regex quote check
cErikson Aug 8, 2019
50ef1ce
forgot then fi
cErikson Aug 8, 2019
0217ee9
Fixed hardcode core count
cErikson Aug 8, 2019
3c6609e
Merge pull request #128 from cErikson/master
nchernia Aug 9, 2019
0ff4593
Merge branch 'master' into enhanced-patterns
nchernia Aug 9, 2019
7bfdb99
Merge pull request #88 from ecsedi/enhanced-patterns
nchernia Aug 9, 2019
a55bfe3
Changed chimeric blacklist to handle quadruple reads and eliminate MT…
nchernia Aug 23, 2019
66e9807
added new handling of four way reads to END block
nchernia Aug 26, 2019
c9de892
Now properly handle quadruple reads. Also eliminated MT check, which …
nchernia Aug 26, 2019
8f7177a
fixing problem in generate site positions when using Python 3.7
nchernia Sep 19, 2019
52847a6
Update bug_report.md
sa501428 Nov 13, 2019
edbe00d
Update custom.md
sa501428 Nov 13, 2019
6403a27
removing repetitive script; the one in misc/ is what should be used
nchernia Nov 25, 2019
df12164
Update juicer.sh
nchernia Apr 17, 2020
cab7978
Files from @suhas-rao
sa501428 Apr 30, 2020
0ecc10e
Change log
nchernia May 11, 2020
d490648
updating usage. note that none is now the default
nchernia May 11, 2020
dee3bf6
Update juicer.sh
nchernia May 12, 2020
f866383
Update juicer.sh
nchernia May 12, 2020
5d2b4a1
code cleanup
sa501428 Jun 8, 2020
5790021
Update README.md
nchernia Jun 12, 2020
9b10bc6
adding in tmpdir for sort call in the collisions dedup
nchernia Jun 22, 2020
652760d
Removing unused LibraryComplexity
nchernia Jun 25, 2020
198a93b
Added in -v nowobble=1 for split_rmdups. This is the only non-whitesp…
nchernia Aug 24, 2020
1a95023
Added justexact flag. Added early exit flag. Consistent with other Ju…
nchernia Aug 24, 2020
e0d1bb7
Minor change to print out help for just exact
nchernia Aug 24, 2020
63c4ae5
suppress too many args error if host returns >1 line
rmdickson Nov 5, 2020
2afef51
Merge pull request #191 from rmdickson/Issue189
nchernia Nov 6, 2020
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34 changes: 34 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
---
name: Bug report
about: Create a report to help us improve
title: ''
labels: bug
assignees: ''

---

**Are you sure this is a bug?**
If unsure, please post your question/situation to the forum first: aidenlab.org/forum.html

**Describe the bug**
A clear and concise description of what the bug is.

**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

**Expected behavior**
A clear and concise description of what you expected to happen.

**Screenshots**
If applicable, add screenshots to help explain your problem.

**Desktop (please complete the following information):**
- OS: [e.g. macOS Mojave, Windows 10, etc]
- Version [e.g. 1.6]

**Additional context**
Add any other context about the problem here.
12 changes: 12 additions & 0 deletions .github/ISSUE_TEMPLATE/custom.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
---
name: Custom issue template
about: Describe this issue template's purpose here.
title: ''
labels: ''
assignees: ''

---


**Are you sure this is an issue?**
Github Issues is reserved for situations that require changes to the codebase. Questions, discussions, etc. should be posted to the forum: aidenlab.org/forum.html
20 changes: 20 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
---
name: Feature request
about: Suggest an idea for this project
title: ''
labels: ''
assignees: ''

---

**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

**Describe the solution you'd like**
A clear and concise description of what you want to happen.

**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.

**Additional context**
Add any other context or screenshots about the feature request here.
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