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Short reads #105

Merged
merged 48 commits into from
Aug 21, 2023
Merged

Short reads #105

merged 48 commits into from
Aug 21, 2023

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rkpfeil
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@rkpfeil rkpfeil commented Aug 17, 2023

Functionalities for correction with short reads

andrewprzh and others added 30 commits June 20, 2023 14:52
@andrewprzh
add option for illumina reads
6aa06a0
@rkpfeil
Functionalities for comparing introns from IsoQuant and Illumina reads
9b3716d
@rkpfeil
Changed default file name for database
7cb37e3
@rkpfeil
Output of number of equal counts
57301ef
@rkpfeil
added first correction of introns with short reads
93dfa19
@rkpfeil
Cosmetic changes
7bc9a1a
@rkpfeil
moved get introns function into the corrector
bd3e294
@rkpfeil
add correction step to process_intergenic
f5aa6a0
@rkpfeil
changed correct_exons to correct_read
c27b933
@rkpfeil
adding second criterion for correcting introns, test
1b5777f
@rkpfeil
Debugging
345e80e
@rkpfeil
Debugging
685c7d3
@rkpfeil
debuggung
5c94942
@rkpfeil
debugging
231e270
@rkpfeil
debugging
c744960
@rkpfeil
debugging
6d5340d
@rkpfeil
added check for introns from short reads longer than the long read
cbf0b46
@rkpfeil
Removing wrong correction
1262ef8
@rkpfeil
third try for correcting based on offsets
bd7ac21
@rkpfeil
correcting through count and difference
a1a3e11
@rkpfeil
correction of difference 4
0083e7b
@rkpfeil
Added statistics for reads and introns. Included skipped exons. Curre…
74a0ff1 
…nt version: 10 without offset 4
@rkpfeil
reverting to version 3 to run on server
e469724
@rkpfeil
switching to read statistics on server
311debc
@rkpfeil
fixed reference db creation
d54ce8b
@rkpfeil
fixed reference db creation
96b7ed9
@rkpfeil
reverting to version 4. intron stats fixed
55f7036
@rkpfeil
corrected false brackets
1e15f80
@rkpfeil
version 5 for stats
248e67f
@rkpfeil
version 6 for stats
f90fa8c
andrewprzh
andrewprzh approved these changes Aug 18, 2023
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looks good to me

src/correction_stats.py Show resolved Hide resolved
src/illumina_exon_corrector.py Outdated Show resolved Hide resolved
@rkpfeil rkpfeil merged commit 064ec5b into master Aug 21, 2023
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@andrewprzh andrewprzh andrewprzh approved these changes

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@rkpfeil @andrewprzh