[med-svn] [Git][med-team/mcaller][master] 9 commits: d/watch: Upstream has first release
Steffen Möller
gitlab at salsa.debian.org
Thu Dec 3 00:18:49 GMT 2020
Steffen Möller pushed to branch master at Debian Med / mcaller
Commits:
d09b9e0c by Steffen Möller at 2020-12-03T00:09:19+01:00
d/watch: Upstream has first release
- - - - -
2c8a9480 by Steffen Möller at 2020-12-03T00:09:44+01:00
New upstream version 1.0
- - - - -
1883235d by Steffen Möller at 2020-12-03T00:09:44+01:00
routine-update: New upstream version
- - - - -
990b3cff by Steffen Möller at 2020-12-03T00:10:12+01:00
Update upstream source from tag 'upstream/1.0'
Update to upstream version '1.0'
with Debian dir 043913077dc4132e18f217373f40bb551002cf93
- - - - -
5795fbab by Steffen Möller at 2020-12-03T00:10:12+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
15e9ecf5 by Steffen Möller at 2020-12-03T00:10:15+01:00
routine-update: Remove trailing whitespace in debian/rules
- - - - -
a0afca77 by Steffen Möller at 2020-12-03T00:10:19+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
f805ec32 by Steffen Möller at 2020-12-03T00:11:22+01:00
routine-update: Ready to upload to unstable
- - - - -
51ab9f38 by Steffen Möller at 2020-12-03T01:17:56+01:00
subject to peer review
- - - - -
14 changed files:
- README.md
- debian/changelog
- debian/control
- + debian/manpages
- debian/mcaller.install
- + debian/mcaller.links
- + debian/mcaller.lintian-overrides
- debian/patches/python2to3.patch
- debian/rules
- debian/tests/run-unit-test
- debian/upstream/metadata
- debian/watch
- testdata/masonread1.eventalign.diffs.6
- testdata/masonread1.eventalign.diffs.6.train
Changes:
=====================================
README.md
=====================================
@@ -139,7 +139,7 @@ Reference fasta, PacBio calls for m6A and a subset of A positions, and eventalig
This will generate the output file testdata/masonread1.eventalign.diffs.6
```
-./make_bed.py -f testdata/masonread1.eventalign.diffs.6 -d 1 -m 0.5
+./make_bed.py -f testdata/masonread1.eventalign.diffs.6 -d 1 -t 0.5
```
Will then generate the output bed file testdata/masonread.methylation.summary.bed with columns chrom, chromStart, chromEnd, context, % methylated, strand, depth of coverage
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-mcaller (0.3+git20200621.90f6389-1) UNRELEASED; urgency=medium
+mcaller (1.0-1) unstable; urgency=medium
* Initial release (Closes: #969558)
@@ -6,5 +6,10 @@ mcaller (0.3+git20200621.90f6389-1) UNRELEASED; urgency=medium
- installation should be done properly - needs setup.py ?!?
- .py in executables (secondary)
- README and test files does seem to be in sync with current code.
+ * New upstream version
+ * Standards-Version: 4.5.1 (routine-update)
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
- -- Steffen Moeller <moeller at debian.org> Fri, 04 Sep 2020 22:28:05 +0200
+ -- Steffen Moeller <moeller at debian.org> Thu, 03 Dec 2020 00:11:06 +0100
=====================================
debian/control
=====================================
@@ -6,8 +6,9 @@ Uploaders: Steffen Moeller <moeller at debian.org>
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all,
- python3-setuptools
-Standards-Version: 4.5.0
+ python3-setuptools,
+ help2man
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/mcaller
Vcs-Git: https://salsa.debian.org/med-team/mcaller.git
Homepage: https://github.com/al-mcintyre/mCaller
@@ -16,7 +17,8 @@ Rules-Requires-Root: no
Package: mcaller
Architecture: all
-Depends: ${python3:Depends},
+Depends: python3,
+ ${python3:Depends},
${misc:Depends},
python3-sklearn,
python3-h5py,
=====================================
debian/manpages
=====================================
@@ -0,0 +1,3 @@
+debian/mCaller.1
+debian/make_bed.1
+debian/compare_genomes.1
=====================================
debian/mcaller.install
=====================================
@@ -1,8 +1,8 @@
-compare_genomes.py usr/bin
-make_bed.py usr/bin
-mCaller.py usr/bin
-extract_contexts.py usr/lib/python3/dist-packages/mCaller
-load_mCaller_data.py usr/lib/python3/dist-packages/mCaller
-plotlib.py usr/lib/python3/dist-packages/mCaller
-read_qual.py usr/lib/python3/dist-packages/mCaller
-train_model.py usr/lib/python3/dist-packages/mCaller
+compare_genomes.py usr/share/mCaller/
+make_bed.py usr/share/mCaller/
+mCaller.py usr/share/mCaller/
+extract_contexts.py usr/share/mCaller/
+load_mCaller_data.py usr/share/mCaller/
+plotlib.py usr/share/mCaller/
+read_qual.py usr/share/mCaller/
+train_model.py usr/share/mCaller/
=====================================
debian/mcaller.links
=====================================
@@ -0,0 +1,6 @@
+/usr/share/mCaller/mCaller.py /usr/bin/mCaller
+/usr/share/mCaller/make_bed.py /usr/bin/make_bed
+/usr/share/mCaller/compare_genomes.py /usr/bin/compare_genomes
+/usr/share/mCaller/mCaller.py /usr/lib/debian-med/bin/mCaller.py
+/usr/share/mCaller/make_bed.py /usr/lib/debian-med/bin/make_bed.py
+/usr/share/mCaller/compare_genomes.py /usr/lib/debian-med/bin/compare_genomes.py
=====================================
debian/mcaller.lintian-overrides
=====================================
@@ -0,0 +1,6 @@
+# It is a "picture"
+mcaller: description-starts-with-leading-spaces
+# The debian-med separate bin for compatibility with .py file endings
+mcaller: breakout-link usr/lib/debian-med/bin/compare_genomes.py -> usr/share/mCaller/compare_genomes.py
+mcaller: breakout-link usr/lib/debian-med/bin/mCaller.py -> usr/share/mCaller/mCaller.py
+mcaller: breakout-link usr/lib/debian-med/bin/make_bed.py -> usr/share/mCaller/make_bed.py
=====================================
debian/patches/python2to3.patch
=====================================
@@ -1,7 +1,7 @@
-Index: mcaller-0.0/compare_genomes.py
+Index: mcaller/compare_genomes.py
===================================================================
---- mcaller-0.0.orig/compare_genomes.py
-+++ mcaller-0.0/compare_genomes.py
+--- mcaller.orig/compare_genomes.py
++++ mcaller/compare_genomes.py
@@ -28,7 +28,7 @@ def compare_by_position(bed1,bed2,xmfa):
t,pval3 = 'none','missing df'
d,pval4 = ks_2samp(pos_dict[0][pos][1],pos_dict[0][pos][1])
@@ -20,10 +20,10 @@ Index: mcaller-0.0/compare_genomes.py
sys.exit(0)
assert os.path.isfile(args.bed1), 'file not found at '+args.bed1
-Index: mcaller-0.0/make_bed.py
+Index: mcaller/make_bed.py
===================================================================
---- mcaller-0.0.orig/make_bed.py
-+++ mcaller-0.0/make_bed.py
+--- mcaller.orig/make_bed.py
++++ mcaller/make_bed.py
@@ -75,7 +75,7 @@ def aggregate_by_pos(meth_fi,aggfi,depth
values_dict = {}
for line in open(meth_fi,'r'):
@@ -63,10 +63,10 @@ Index: mcaller-0.0/make_bed.py
aggregate_by_pos(args.mCaller_file,output_file,args.min_read_depth,args.mod_threshold,args.positions,args.control,args.vo,args.gff,args.ref,args.plot,args.plotdir,args.plotsummary)
-Index: mcaller-0.0/extract_contexts.py
+Index: mcaller/extract_contexts.py
===================================================================
---- mcaller-0.0.orig/extract_contexts.py
-+++ mcaller-0.0/extract_contexts.py
+--- mcaller.orig/extract_contexts.py
++++ mcaller/extract_contexts.py
@@ -2,8 +2,7 @@ from collections import defaultdict
from Bio import SeqIO
import scipy.stats as ss
@@ -160,10 +160,10 @@ Index: mcaller-0.0/extract_contexts.py
diff_col = [[] for i in range(k)]
sys.exit(0)
-Index: mcaller-0.0/mCaller.py
+Index: mcaller/mCaller.py
===================================================================
---- mcaller-0.0.orig/mCaller.py
-+++ mcaller-0.0/mCaller.py
+--- mcaller.orig/mCaller.py
++++ mcaller/mCaller.py
@@ -3,8 +3,8 @@
#Alexa McIntyre, 2016-2018
@@ -175,10 +175,10 @@ Index: mcaller-0.0/mCaller.py
#import _pickle as cPickle
from collections import defaultdict
import numpy as np
-Index: mcaller-0.0/train_model.py
+Index: mcaller/train_model.py
===================================================================
---- mcaller-0.0.orig/train_model.py
-+++ mcaller-0.0/train_model.py
+--- mcaller.orig/train_model.py
++++ mcaller/train_model.py
@@ -1,5 +1,4 @@
-import cPickle
-#import _pickle as cPickle
@@ -217,3 +217,13 @@ Index: mcaller-0.0/train_model.py
modfi.close()
return models
+Index: mcaller/plotlib.py
+===================================================================
+--- mcaller.orig/plotlib.py
++++ mcaller/plotlib.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import matplotlib.pyplot as plt
=====================================
debian/rules
=====================================
@@ -2,21 +2,29 @@
DH_VERBOSE := 1
export LC_ALL=C.UTF-8
+UVERSION=`head -n1 debian/changelog |cut -f1 -d- | cut -f2 -d'(' `
include /usr/share/dpkg/default.mk
%:
dh $@ --with python3
+override_dh_auto_build:
+ dh_auto_build
+ help2man ./mCaller.py --version-string=$(UVERSION) --no-info > debian/mCaller.1
+ help2man ./make_bed.py --version-string=$(UVERSION) --no-info > debian/make_bed.1
+ help2man ./compare_genomes.py --version-string=$(UVERSION) --no-info > debian/compare_genomes.1
+
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- ./mCaller.py -p testdata/test_positions_A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq
- ./mCaller.py -p testdata/test_positions_m6A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq
- #./make_bed.py -f testdata/masonread1.eventalign.diffs.6 -d 1 -m 0.5
+ ./mCaller.py -p testdata/test_positions_A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq
+ ./mCaller.py -p testdata/test_positions_m6A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq
+ #./make_bed.py -f testdata/masonread1.eventalign.diffs.6 -d 1 -m 0.5
./mCaller.py -p testdata/test_positions.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -t 4 --train -f testdata/masonread1.fastq
endif
override_dh_auto_clean:
dh_auto_clean
- rm -f model_NN_6_m6A.pkl
+ rm -f model_NN_6_m6A.pkl testdata/masonread1.eventalign.diffs.6 testdata/masonread1.eventalign.diffs.6.train
rm -rf __pycache__
+ rm -f debian/*.1
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
set -e
-pkg=#PACKAGENAME#
+pkg=mcaller
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/al-mcintyre/mCaller/issues
+Bug-Submit: https://github.com/al-mcintyre/mCaller/issues/new
Reference:
- Author:
Title:
@@ -17,3 +19,5 @@ Registry:
Entry:
- Name: bio.tools
Entry:
+Repository: https://github.com/al-mcintyre/mCaller.git
+Repository-Browse: https://github.com/al-mcintyre/mCaller
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
version=4
-opts="mode=git,pretty=0.3+git%cd.%h" \
- https://github.com/al-mcintyre/mCaller.git HEAD
+#opts="mode=git,pretty=0.3+git%cd.%h" https://github.com/al-mcintyre/mCaller.git HEAD
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%mcaller-$1.tar.gz%" \
+ https://github.com/al-mcintyre/mCaller/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
=====================================
testdata/masonread1.eventalign.diffs.6
=====================================
@@ -1,35 +1,9 @@
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13673 CATTAMCAATC 1.1,-0.236666666667,0.28,1.17,-0.02,0.67,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13861 GCCCGMTATAT -0.53,-2.56,-0.46,-2.09,-5.4,1.05,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14331 TTTTGMGATCC 0.06,-1.6,-3.48,1.365,1.06,3.94,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14352 TCGTGMATGCA 2.98,1.47,-2.14,5.63,1.07,5.135,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14444 TAAAAMAGAGA -0.68,-0.74,-0.585,-0.48,-0.815,-1.08,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14528 ATCAAMCCGAG 4.025,-0.115,-1.02,-0.48,0.173333333333,1.19,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14836 GCTTTMGCAAA -1.37333333333,0.18,-0.613333333333,-1.43,-0.005,-4.32,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15536 TGCGTMTTCAA -0.1,2.23,-2.058,2.78,-0.68,0.51,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15630 CTTCCMGCCAC -2.72,-1.03,-0.14,2.625,1.0375,-1.075,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16154 AGATAMTAAAT -2.38,-1.03,-2.88333333333,-0.59,-4.31,-4.94,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16209 TCTTAMTAACA -0.3075,4.23,0.88,0.326666666667,-4.165,0.93,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16397 GTATTMTCAAT -0.63,-2.97,-0.736666666667,-2.71,-1.12,-3.25111111111,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16979 AAATGMGATTT -1.44,-5.03,1.445,0.4,-0.588,-0.55,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17243 AGTAGMTTGAT -1.44333333333,-0.02,-0.0366666666667,-0.55,0.64,-2.71,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17283 ACTTAMCCGGT -1.23,-1.635,-0.24,1.10333333333,-2.215,-2.93,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17486 AGCATMTTTAT -0.21,0.075,-1.30833333333,4.15,-0.3,-0.215,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17796 GTTATMTGCAA -1.355,-0.34,-1.86333333333,-1.87,-1.265,-1.22,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17923 GGTAAMAATTT -5.64,-3.6,-5.13,-0.255,0.4,0.73,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18402 GTGACMGTTTT -1.14,0.94,-4.55,2.0,-0.34,-2.71,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18488 GGCTTMTTTTA 1.02,-2.38,0.915,0.05,1.75,0.8875,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18575 GGATGMAAGAA -0.56,-3.505,1.02,-1.55,-0.714,-0.4825,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18804 ATATTMTGCAT 3.49,1.3,-1.495,-2.3,-1.2,-0.62,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18828 TCGTGMAAAAT -1.405,-2.96,-3.1,0.57,-0.433333333333,-1.44,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 20255 AGGCCMTTCAA -2.15,1.885,2.58,-0.36,4.26,-2.4625,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 20591 AATCAMAAGAA 1.485,4.095,-1.12,-0.91,-0.62,1.17,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 21448 TACTTMCCGCA 1.095,0.78,-2.38,1.47,-1.715,-0.828333333333,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22359 AACTCMAGGTA -3.59,1.85666666667,-0.96,0.0671428571429,0.573333333333,1.21,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22558 GAAGAMTCAAC 1.005,3.05,3.07,0.4625,0.32,-0.603333333333,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 23402 GGATTMTTTCA -0.19,-1.68,-2.3,0.56,-1.41,1.48,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24474 CTGGAMAAAGC -1.13,-1.67,-1.1,-0.5775,0.42,1.0225,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24629 GGGCCMTTACC 0.005,-0.295,-0.54,3.96,1.47,0.065,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24715 GGTGGMTGAAT 3.255,3.925,0.04,-0.156,-1.01,1.35333333333,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24770 GGTTAMCGCGT -0.08,-1.36666666667,0.84,-0.545,-3.22,-1.53,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 25340 TGTGGMGAAAC -1.74,-2.56,-2.0775,1.84,-0.1,-0.3,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 25919 AGAACMCTTTC 1.92,2.75,1.59,1.64333333333,1.59,1.27,7.05526534938 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13791 GTAAGMTCCCT -0.4066666666666667,1.6099999999999999,-1.6866666666666665,6.67,-4.55,1.775,7.055265349382997 - m6A 0.67
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14329 TTGAGMTCCGC -3.48,1.365,1.06,3.94,1.6,0.98,7.055265349382997 - m6A 0.52
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14827 AACAGMTCTCC -2.38,-2.11,-1.45,-1.4900000000000002,-1.98,0.53,7.055265349382997 - A 0.08
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15249 GCTTGMTCTCT 0.65,2.7,-3.18,1.41,0.76,3.43,7.055265349382997 - A 0.46
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 19419 CACAGMTCTAC 1.41,-0.9933333333333332,-2.08,-3.42,-1.5650000000000002,-2.332,7.055265349382997 - A 0.12
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 21759 TGGCGMTCCCT -1.502,-2.01,-2.26,0.5433333333333333,-7.57,-3.11,7.055265349382997 - A 0.26
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22161 CAGCGMTCCGG 2.13,0.7219999999999999,-0.44,-0.08499999999999996,3.9250000000000003,2.86,7.055265349382997 - m6A 0.65
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 23875 GTCCGMTCCGA 6.19,-2.07,0.695,2.71,3.575,3.1566666666666667,7.055265349382997 - A 0.44
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24559 GCTCAMCGGCT -0.53,1.9366666666666665,-1.86,0.58,4.6450000000000005,1.17,7.055265349382997 - m6A 0.77
=====================================
testdata/masonread1.eventalign.diffs.6.train
=====================================
@@ -1,44 +1,44 @@
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13673 CATTAMCAATC 1.1,-0.236666666667,0.28,1.17,-0.02,0.67,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16979 AAATGMGATTT -1.44,-5.03,1.445,0.4,-0.588,-0.55,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 20255 AGGCCMTTCAA -2.15,1.885,2.58,-0.36,4.26,-2.4625,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 23402 GGATTMTTTCA -0.19,-1.68,-2.3,0.56,-1.41,1.48,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13791 GTAAGMTCCCT -0.406666666667,1.61,-1.68666666667,6.67,-4.55,1.775,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17243 AGTAGMTTGAT -1.44333333333,-0.02,-0.0366666666667,-0.55,0.64,-2.71,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13861 GCCCGMTATAT -0.53,-2.56,-0.46,-2.09,-5.4,1.05,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 20591 AATCAMAAGAA 1.485,4.095,-1.12,-0.91,-0.62,1.17,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17283 ACTTAMCCGGT -1.23,-1.635,-0.24,1.10333333333,-2.215,-2.93,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 23875 GTCCGMTCCGA 6.19,-2.07,0.695,2.71,3.575,3.15666666667,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17486 AGCATMTTTAT -0.21,0.075,-1.30833333333,4.15,-0.3,-0.215,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14329 TTGMGMTCCGC -3.48,1.365,1.06,3.94,1.6,0.98,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14331 TTTTGMGMTCC 0.06,-1.6,-3.48,1.365,1.06,3.94,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14352 TCGTGMATGCA 2.98,1.47,-2.14,5.63,1.07,5.135,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17796 GTTATMTGCAA -1.355,-0.34,-1.86333333333,-1.87,-1.265,-1.22,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24474 CTGGAMAAAGC -1.13,-1.67,-1.1,-0.5775,0.42,1.0225,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14444 TAAAAMAGAGA -0.68,-0.74,-0.585,-0.48,-0.815,-1.08,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17923 GGTAAMAATTT -5.64,-3.6,-5.13,-0.255,0.4,0.73,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 21448 TACTTMCCGCA 1.095,0.78,-2.38,1.47,-1.715,-0.828333333333,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24559 GCTCAMCGGCT -0.53,1.93666666667,-1.86,0.58,4.645,1.17,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14528 ATCAAMCCGAG 4.025,-0.115,-1.02,-0.48,0.173333333333,1.19,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24629 GGGCCMTTACC 0.005,-0.295,-0.54,3.96,1.47,0.065,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18402 GTGACMGTTTT -1.14,0.94,-4.55,2.0,-0.34,-2.71,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 21759 TGGCGMTCCCT -1.502,-2.01,-2.26,0.543333333333,-7.57,-3.11,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24715 GGTGGMTGAAT 3.255,3.925,0.04,-0.156,-1.01,1.35333333333,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18488 GGCTTMTTTTA 1.02,-2.38,0.915,0.05,1.75,0.8875,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14827 AACAGMTCTCC -2.38,-2.11,-1.45,-1.49,-1.98,0.53,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24770 GGTTAMCGCGT -0.08,-1.36666666667,0.84,-0.545,-3.22,-1.53,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22161 CAGCGMTCCGG 2.13,0.722,-0.44,-0.085,3.925,2.86,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18575 GGATGMAAGAA -0.56,-3.505,1.02,-1.55,-0.714,-0.4825,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14836 GCTTTMGCAAA -1.37333333333,0.18,-0.613333333333,-1.43,-0.005,-4.32,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 25340 TGTGGMGAAAC -1.74,-2.56,-2.0775,1.84,-0.1,-0.3,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15249 GCTTGMTCTCT 0.65,2.7,-3.18,1.41,0.76,3.43,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22359 AACTCMAGGTA -3.59,1.85666666667,-0.96,0.0671428571429,0.573333333333,1.21,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18804 ATATTMTGCAT 3.49,1.3,-1.495,-2.3,-1.2,-0.62,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18828 TCGTGMAAAAT -1.405,-2.96,-3.1,0.57,-0.433333333333,-1.44,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22558 GAAGAMTCAAC 1.005,3.05,3.07,0.4625,0.32,-0.603333333333,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 25919 AGAACMCTTTC 1.92,2.75,1.59,1.64333333333,1.59,1.27,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15536 TGCGTMTTCAA -0.1,2.23,-2.058,2.78,-0.68,0.51,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15630 CTTCCMGCCAC -2.72,-1.03,-0.14,2.625,1.0375,-1.075,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 19419 CACAGMTCTAC 1.41,-0.993333333333,-2.08,-3.42,-1.565,-2.332,7.05526534938 - m6A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16154 AGATAMTAAAT -2.38,-1.03,-2.88333333333,-0.59,-4.31,-4.94,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16209 TCTTAMTAACA -0.3075,4.23,0.88,0.326666666667,-4.165,0.93,7.05526534938 - A
-26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16397 GTATTMTCAAT -0.63,-2.97,-0.736666666667,-2.71,-1.12,-3.25111111111,7.05526534938 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13673 CATTAMCAATC 1.1,-0.23666666666666666,0.28,1.17,-0.02,0.6699999999999999,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13791 GTAAGMTCCCT -0.4066666666666667,1.6099999999999999,-1.6866666666666665,6.67,-4.55,1.775,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 13861 GCCCGMTATAT -0.53,-2.56,-0.45999999999999996,-2.09,-5.4,1.05,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14329 TTGMGMTCCGC -3.48,1.365,1.06,3.94,1.6,0.98,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14331 TTTTGMGMTCC 0.06,-1.5999999999999999,-3.48,1.365,1.06,3.94,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14352 TCGTGMATGCA 2.98,1.47,-2.14,5.63,1.07,5.135,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14444 TAAAAMAGAGA -0.68,-0.74,-0.585,-0.48,-0.815,-1.08,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14528 ATCAAMCCGAG 4.0249999999999995,-0.11499999999999999,-1.02,-0.48,0.17333333333333337,1.19,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14827 AACAGMTCTCC -2.38,-2.11,-1.45,-1.4900000000000002,-1.98,0.53,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 14836 GCTTTMGCAAA -1.3733333333333333,0.17999999999999994,-0.6133333333333334,-1.43,-0.0050000000000000044,-4.32,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15249 GCTTGMTCTCT 0.65,2.7,-3.18,1.41,0.76,3.43,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15536 TGCGTMTTCAA -0.1,2.23,-2.058,2.78,-0.68,0.51,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 15630 CTTCCMGCCAC -2.7199999999999998,-1.03,-0.14,2.625,1.0375,-1.075,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16154 AGATAMTAAAT -2.38,-1.03,-2.8833333333333333,-0.59,-4.31,-4.94,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16209 TCTTAMTAACA -0.3075,4.23,0.88,0.32666666666666666,-4.165,0.93,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16397 GTATTMTCAAT -0.63,-2.97,-0.7366666666666667,-2.71,-1.1199999999999999,-3.251111111111111,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 16979 AAATGMGATTT -1.44,-5.03,1.4449999999999998,0.4000000000000001,-0.588,-0.55,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17243 AGTAGMTTGAT -1.4433333333333334,-0.020000000000000018,-0.0366666666666667,-0.5499999999999999,0.64,-2.71,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17283 ACTTAMCCGGT -1.23,-1.635,-0.24,1.1033333333333333,-2.215,-2.93,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17486 AGCATMTTTAT -0.21,0.07500000000000001,-1.3083333333333333,4.15,-0.3,-0.21500000000000002,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17796 GTTATMTGCAA -1.355,-0.34,-1.8633333333333333,-1.87,-1.2650000000000001,-1.22,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 17923 GGTAAMAATTT -5.64,-3.6,-5.13,-0.255,0.4,0.73,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18402 GTGACMGTTTT -1.1400000000000001,0.94,-4.55,2.0,-0.34,-2.71,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18488 GGCTTMTTTTA 1.02,-2.38,0.915,0.05,1.75,0.8875000000000001,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18575 GGATGMAAGAA -0.56,-3.505,1.02,-1.55,-0.7139999999999999,-0.4825,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18804 ATATTMTGCAT 3.49,1.3,-1.4949999999999999,-2.3,-1.2,-0.62,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 18828 TCGTGMAAAAT -1.405,-2.96,-3.1,0.5699999999999998,-0.43333333333333335,-1.44,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 19419 CACAGMTCTAC 1.41,-0.9933333333333332,-2.08,-3.42,-1.5650000000000002,-2.332,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 20255 AGGCCMTTCAA -2.15,1.8849999999999998,2.58,-0.36,4.26,-2.4625,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 20591 AATCAMAAGAA 1.485,4.095000000000001,-1.12,-0.91,-0.62,1.17,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 21448 TACTTMCCGCA 1.095,0.78,-2.38,1.47,-1.7149999999999999,-0.8283333333333335,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 21759 TGGCGMTCCCT -1.502,-2.01,-2.26,0.5433333333333333,-7.57,-3.11,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22161 CAGCGMTCCGG 2.13,0.7219999999999999,-0.44,-0.08499999999999996,3.9250000000000003,2.86,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22359 AACTCMAGGTA -3.59,1.8566666666666667,-0.9600000000000001,0.06714285714285717,0.5733333333333334,1.21,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 22558 GAAGAMTCAAC 1.0050000000000001,3.05,3.07,0.46249999999999997,0.32,-0.6033333333333334,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 23402 GGATTMTTTCA -0.18999999999999992,-1.6799999999999997,-2.3,0.56,-1.41,1.48,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 23875 GTCCGMTCCGA 6.19,-2.07,0.695,2.71,3.575,3.1566666666666667,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24474 CTGGAMAAAGC -1.1300000000000001,-1.67,-1.1,-0.5774999999999999,0.42,1.0225,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24559 GCTCAMCGGCT -0.53,1.9366666666666665,-1.86,0.58,4.6450000000000005,1.17,7.055265349382997 - m6A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24629 GGGCCMTTACC 0.0050000000000000044,-0.29500000000000004,-0.54,3.96,1.47,0.06499999999999995,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24715 GGTGGMTGAAT 3.255,3.925,0.03999999999999998,-0.15599999999999997,-1.01,1.3533333333333333,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 24770 GGTTAMCGCGT -0.07999999999999996,-1.3666666666666665,0.84,-0.5449999999999999,-3.22,-1.53,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 25340 TGTGGMGAAAC -1.74,-2.56,-2.0774999999999997,1.84,-0.09999999999999998,-0.3,7.055265349382997 - A
+ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template 25919 AGAACMCTTTC 1.92,2.75,1.59,1.6433333333333333,1.59,1.27,7.055265349382997 - A
View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/5116e888737a0c7c7e949822a115c456f7a31abd...51ab9f3890c5f27fb1351c333905ab2b8dc5b09a
--
View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/5116e888737a0c7c7e949822a115c456f7a31abd...51ab9f3890c5f27fb1351c333905ab2b8dc5b09a
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201203/52cab221/attachment-0001.html>
More information about the debian-med-commit
mailing list