<commit_before>[tophat-config]
bowtieversion=1
referencebuild=
genebuild=
species=
referenceloc=
referenceindex=genome
transcriptomeindex=transcriptome
tophatpostindex=tophatpost.genome
ensgene=ensGene.txt
refgene=refGene.txt
blastdb=blast
blastn=
normalfusionslist=normal-fusions
bowtie1path=
bowtie2path=
tophatpath=
librarytype=fr-unstranded

[tophat-parameters]
output-dir=./tophat_out
bowtie1=N
read-mismatches=2
read-gap-length=2
read-edit-dist=2
read-realign-edit-dist=3
min-anchor=8
splice-mismatches=0
min-intron-length=50
max-intron-length=500000
max-multihits=20
transcriptome-max-hits=60
max-insertion-length=3
max-deletion-length=3
library-type=fr-unstranded
num-threads=1
transcriptome-index=
transcriptome-only=N
GTF=
rawjuncs=
insertions=
deletions=
mate-inner-dist=50
mate-std-dev=20
no-novel-juncs=N
no-novel-indels=N
no-gtf-juncs=N
no-coverage-search=Y
coverage-search=N
suppress-hits=N
solexa-quals=N
solexa1.3-quals=N
phred64-quals=N
quals=N
color=N
microexon-search=N
keeptmp=N
tmpdir=
zpacker=gzip
unmapped-fifo=N
report-secondary-alignments=N
no-discordant=N
no-mixed=N
segment-mismatches=2
segment-length=25
min-coverage-intron=50
max-coverage-intron=20000
min-segment-intron=50
max-segment-intron=500000
no-sort-bam=N
no-convert-bam=N
keep-fasta-order=Y
allow-partial-mapping=N
rg-id=
rg-sample=
rg-library=
rg-description=
rg-platform-unit=
rg-center=
rg-date=
rg-platform=

[tophat-fusion-parameters]
fusion-search=Y
fusion-anchor-length=13
fusion-min-dist=1000000
fusion-read-mismatches=2
fusion-multireads=2
fusion-multipairs=2
fusion-ignore-chromosomes=

[tophat-post-parameters]
output-dir=./tophatfusion_out
num-fusion-reads=1
num-fusion-pairs=2
num-fusion-both=5
fusion-read-mismatches=2
fusion-multireads=2
non-human=N
num-threads=1
no-filter-by-annotation=N
skip-fusion-kmer=N
skip-filter-fusion=N
skip-blast=N
skip-read-dist=N
skip-html=N
tex-table=N
<commit_msg>tophat-fusion-post now skips read dist step, which our infuse pipeline does not care and not in final html report anyway. close #24<commit_after>[tophat-config]
bowtieversion=1
referencebuild=
genebuild=
species=
referenceloc=
referenceindex=genome
transcriptomeindex=transcriptome
tophatpostindex=tophatpost.genome
ensgene=ensGene.txt
refgene=refGene.txt
blastdb=blast
blastn=
normalfusionslist=normal-fusions
bowtie1path=
bowtie2path=
tophatpath=
librarytype=fr-unstranded

[tophat-parameters]
output-dir=./tophat_out
bowtie1=N
read-mismatches=2
read-gap-length=2
read-edit-dist=2
read-realign-edit-dist=3
min-anchor=8
splice-mismatches=0
min-intron-length=50
max-intron-length=500000
max-multihits=20
transcriptome-max-hits=60
max-insertion-length=3
max-deletion-length=3
library-type=fr-unstranded
num-threads=1
transcriptome-index=
transcriptome-only=N
GTF=
rawjuncs=
insertions=
deletions=
mate-inner-dist=50
mate-std-dev=20
no-novel-juncs=N
no-novel-indels=N
no-gtf-juncs=N
no-coverage-search=Y
coverage-search=N
suppress-hits=N
solexa-quals=N
solexa1.3-quals=N
phred64-quals=N
quals=N
color=N
microexon-search=N
keeptmp=N
tmpdir=
zpacker=gzip
unmapped-fifo=N
report-secondary-alignments=N
no-discordant=N
no-mixed=N
segment-mismatches=2
segment-length=25
min-coverage-intron=50
max-coverage-intron=20000
min-segment-intron=50
max-segment-intron=500000
no-sort-bam=N
no-convert-bam=N
keep-fasta-order=Y
allow-partial-mapping=N
rg-id=
rg-sample=
rg-library=
rg-description=
rg-platform-unit=
rg-center=
rg-date=
rg-platform=

[tophat-fusion-parameters]
fusion-search=Y
fusion-anchor-length=13
fusion-min-dist=1000000
fusion-read-mismatches=2
fusion-multireads=2
fusion-multipairs=2
fusion-ignore-chromosomes=

[tophat-post-parameters]
output-dir=./tophatfusion_out
num-fusion-reads=1
num-fusion-pairs=2
num-fusion-both=5
fusion-read-mismatches=2
fusion-multireads=2
non-human=N
num-threads=1
no-filter-by-annotation=N
skip-fusion-kmer=N
skip-filter-fusion=N
skip-blast=N
skip-read-dist=Y
skip-html=N
tex-table=N

{'fraction_non_alphanumeric': 0.12327718223583461, 'fraction_numerical': 0.03573251659009699, 'mean_word_length': 6.917171717171717, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6681561', 'n_tokens_mistral': 1789, 'n_tokens_neox': 1609, 'n_words': 229}