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taoliu

upload missing barcodes.txt for testing

Feb 17, 2025

95f13c7 · Feb 17, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
standard_results_50kcontigs		standard_results_50kcontigs	update hmmratac narrowpeak output since we now allow some short peaks	May 14, 2024
standard_results_bdgbroadcall		standard_results_bdgbroadcall	update gappedPeak output	Sep 6, 2024
standard_results_bdgcmp		standard_results_bdgcmp	Fix /2 or //2 issue. Add standard outputs from MACS2 python2 version …	Oct 1, 2019
standard_results_bdgdiff		standard_results_bdgdiff	update standard output from cmdline	Feb 5, 2021
standard_results_bdgopt		standard_results_bdgopt	update standard output from cmdline	Feb 5, 2021
standard_results_bdgpeakcall		standard_results_bdgpeakcall	use '%5g' for printing all float values; update testing results	Mar 17, 2020
standard_results_callpeak_broad		standard_results_callpeak_broad	update gappedPeak output	Sep 6, 2024
standard_results_callpeak_frag		standard_results_callpeak_frag	enable FRAG support in callpeak and pileup	Feb 15, 2025
standard_results_callpeak_narrow		standard_results_callpeak_narrow	update standard output from cmdline	Feb 5, 2021
standard_results_callpeak_narrow_revert		standard_results_callpeak_narrow_revert	Fix /2 or //2 issue. Add standard outputs from MACS2 python2 version …	Oct 1, 2019
standard_results_callpeak_pe_broad		standard_results_callpeak_pe_broad	update gappedPeak output	Sep 6, 2024
standard_results_callpeak_pe_narrow		standard_results_callpeak_pe_narrow	use float64_t explicitly	Mar 24, 2020
standard_results_callvar		standard_results_callvar	update gappedPeak output	Sep 6, 2024
standard_results_cmbreps		standard_results_cmbreps	update standard output from cmdline	Feb 5, 2021
standard_results_filterdup		standard_results_filterdup	Fix /2 or //2 issue. Add standard outputs from MACS2 python2 version …	Oct 1, 2019
standard_results_hmmratac		standard_results_hmmratac	let hmmratac output narrowpeak with summit and score from foldchange …	May 16, 2024
standard_results_pileup		standard_results_pileup	Fix /2 or //2 issue. Add standard outputs from MACS2 python2 version …	Oct 1, 2019
standard_results_predictd		standard_results_predictd	update standard output from cmdline	Feb 5, 2021
standard_results_refinepeak		standard_results_refinepeak	update standard output from cmdline	Feb 5, 2021
CTCF_12878_5M.bed.gz		CTCF_12878_5M.bed.gz	python profiler and cython profiler added	Oct 30, 2019
CTCF_PE_CTRL_chr22_50k.bam		CTCF_PE_CTRL_chr22_50k.bam	Further reduce testing filesize. Update test.sh script.	Sep 30, 2019
CTCF_PE_CTRL_chr22_50k.bam.bai		CTCF_PE_CTRL_chr22_50k.bam.bai	.bai files for BAM PE	Mar 11, 2021
CTCF_PE_CTRL_chr22_50k.bedpe.gz		CTCF_PE_CTRL_chr22_50k.bedpe.gz	Further reduce testing filesize. Update test.sh script.	Sep 30, 2019
CTCF_PE_ChIP_chr22_50k.bam		CTCF_PE_ChIP_chr22_50k.bam	Further reduce testing filesize. Update test.sh script.	Sep 30, 2019
CTCF_PE_ChIP_chr22_50k.bam.bai		CTCF_PE_ChIP_chr22_50k.bam.bai	.bai files for BAM PE	Mar 11, 2021
CTCF_PE_ChIP_chr22_50k.bedpe.gz		CTCF_PE_ChIP_chr22_50k.bedpe.gz	Further reduce testing filesize. Update test.sh script.	Sep 30, 2019
CTCF_SE_CTRL_chr22_50k.bed.gz		CTCF_SE_CTRL_chr22_50k.bed.gz	Further reduce testing filesize. Update test.sh script.	Sep 30, 2019
CTCF_SE_ChIP_chr22_50k.bed.gz		CTCF_SE_ChIP_chr22_50k.bed.gz	Further reduce testing filesize. Update test.sh script.	Sep 30, 2019
Input_12878_5M.bed.gz		Input_12878_5M.bed.gz	python profiler and cython profiler added	Oct 30, 2019
barcodes.txt		barcodes.txt	upload missing barcodes.txt for testing	Feb 17, 2025
callvar_testing.narrowPeak		callvar_testing.narrowPeak	modify callvar cmdlinetest files	Mar 11, 2021
cmdlinetest		cmdlinetest	enable FRAG support in callpeak and pileup	Feb 15, 2025
cmdlinetest-nohmmratac		cmdlinetest-nohmmratac	explictly use Python version 3	Feb 23, 2024
contigs50k.bed.gz		contigs50k.bed.gz	Related to #313. Enable --buffer-size for filterdup, pileup, randsamp…	Sep 19, 2019
hg19.len		hg19.len	Testing scripts.	Oct 28, 2013
jaccard.py		jaccard.py	enable FRAG support in callpeak and pileup	Feb 15, 2025
large_training_data.txt		large_training_data.txt	unittest for hmmr_hmm codes; remove around since it will cause 0	Sep 30, 2022
large_training_lengths.txt		large_training_lengths.txt	unittest for hmmr_hmm codes; remove around since it will cause 0	Sep 30, 2022
prockreport		prockreport	retire old py2 era hashtable.pyx; add CPU/mem usage test to test.sh	Oct 31, 2019
pyprofile		pyprofile	explictly use Python version 3	Feb 23, 2024
pyprofile_stat		pyprofile_stat	remove khash and stick to Python3 dict; move cached pscore/logLR func…	Nov 2, 2019
small_prediction_data.txt		small_prediction_data.txt	unit test for hmm_predict	Feb 17, 2024
small_prediction_lengths.txt		small_prediction_lengths.txt	unit test for hmm_predict	Feb 17, 2024
small_prediction_results.txt		small_prediction_results.txt	update standard prediction results	Feb 27, 2024
small_prediction_results_poisson.txt		small_prediction_results_poisson.txt	add test for hmm poisson	Mar 13, 2024
test.fragments.tsv.gz		test.fragments.tsv.gz	enable FRAG support in callpeak and pileup	Feb 15, 2025
test_BAMBAI.py		test_BAMBAI.py	BAMaccessor with BAI support is implemented with unit testing	Mar 11, 2021
test_BedGraph.py		test_BedGraph.py	1. implement function for PETrackI/II; 2. blacklisted regions will be…	Feb 12, 2025
test_BedGraphIO.py		test_BedGraphIO.py	update testing scripts	Aug 9, 2019
test_CallPeakUnit.py		test_CallPeakUnit.py	update testing scripts	Aug 9, 2019
test_FixWidthTrack.py		test_FixWidthTrack.py	rename package name Data to Signal	Nov 25, 2020
test_HMMR_HMM.py		test_HMMR_HMM.py	skip hmm unittest for now	Mar 2, 2024
test_HMMR_poisson.py		test_HMMR_poisson.py	implement PETrackII for fragment files from scATAC experiments	Oct 15, 2024
test_PairedEndTrack.py		test_PairedEndTrack.py	1. implement function for PETrackI/II; 2. blacklisted regions will be…	Feb 12, 2025
test_Parser.py		test_Parser.py	enable FRAG support in callpeak and pileup	Feb 15, 2025
test_PeakDetect.py		test_PeakDetect.py	update testing scripts	Aug 9, 2019
test_PeakIO.py		test_PeakIO.py	implement PETrackII for fragment files from scATAC experiments	Oct 15, 2024
test_PeakModel.py		test_PeakModel.py	update testing scripts	Aug 9, 2019
test_Pileup.py		test_Pileup.py	implement PETrackII for fragment files from scATAC experiments	Oct 15, 2024
test_Prob.py		test_Prob.py	rename package name Data to Signal	Nov 25, 2020
test_Region.py		test_Region.py	add function in Region.py to find intersection;made a jaccard.py to c…	Feb 12, 2024
test_ScoreTrack.py		test_ScoreTrack.py	rewrite scoretrack.py	Oct 18, 2024
test_SignalProcessing.py		test_SignalProcessing.py	skip the test on SignalProcessing	May 14, 2024
test_online.py		test_online.py	online algo test	Feb 22, 2022
tiny.bam		tiny.bam	Tiny input files for testing Parser.pyx.	Dec 12, 2019
tiny.bam.bai		tiny.bam.bai	bai support and unit testing	Mar 8, 2021
tiny.bed.gz		tiny.bed.gz	Tiny input files for testing Parser.pyx.	Dec 12, 2019
tiny.bedpe.gz		tiny.bedpe.gz	Tiny input files for testing Parser.pyx.	Dec 12, 2019
tiny.sam.gz		tiny.sam.gz	Tiny input files for testing Parser.pyx.	Dec 12, 2019
yeast_500k_SRR1822137.bam		yeast_500k_SRR1822137.bam	add testing data for hmmratac from the first 500k read pairs of SRR18…	Jun 3, 2022
yeast_500k_SRR1822137.bedpe.gz		yeast_500k_SRR1822137.bedpe.gz	add option for hmmratac to use BEDPE files as input	Aug 2, 2023
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