Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / epi2me-labs/modbam2bed issues and pull requests

#72 - Fix segmentation fault when accessing a non-existent chromosome

Pull Request - State: closed - Opened by hyeshik 4 months ago

#70 - modbam2bed N_filt

Issue - State: closed - Opened by Houssem-der 7 months ago - 3 comments

#69 - 6mA Mod calling in bacterial Data

Issue - State: closed - Opened by AzlanNI 10 months ago - 1 comment

#68 - Adding --aggregate flag does not result in aggregate behavior

Issue - State: closed - Opened by ddubocan 12 months ago - 1 comment

#67 - ERROR: --highthreshold must be larger than --lowthreshold

Issue - State: closed - Opened by Baix7 about 1 year ago - 1 comment

#66 - Dependencies

Issue - State: closed - Opened by NickNCL about 1 year ago - 1 comment

#65 - Warning message inquiry

Issue - State: closed - Opened by nsgarcia27 about 1 year ago - 1 comment

#64 - Diffrent output size for different insert bams?

Issue - State: closed - Opened by assafgrw over 1 year ago - 1 comment

#63 - Fix compilation when NOTHREADS=1

Pull Request - State: closed - Opened by robertaboukhalil over 1 year ago - 2 comments

#62 - visualize in IGV

Issue - State: closed - Opened by sujunhao over 1 year ago - 1 comment

#61 - Modified-Base calling of pod5 files with Dorado, what's next ?

Issue - State: closed - Opened by 120985 over 1 year ago - 1 comment

#60 - Correct workflow for extracting modified bases from bonito calls

Issue - State: closed - Opened by jorisbalc over 1 year ago - 1 comment

#59 - modbampy

Issue - State: closed - Opened by keenhl over 1 year ago - 2 comments

#58 - Modbampy Python package

Issue - State: closed - Opened by keenhl over 1 year ago - 1 comment

#57 - Removal of setting canonical and mod thresholds

Issue - State: closed - Opened by pwh124 over 1 year ago - 1 comment

#56 - how is coverage calculated

Issue - State: closed - Opened by xiaoyunguo over 1 year ago - 1 comment

#55 - Is there a way to mimic the "edge_filter" behavior of megalodon in modbam2bed?

Issue - State: closed - Opened by billytcl over 1 year ago - 2 comments

#54 - version

Issue - State: closed - Opened by rl4940 over 1 year ago - 4 comments

#53 - `undefined symbol: inflate` for modbampy

Issue - State: closed - Opened by PanZiwei over 1 year ago - 2 comments

#52 - Symbol lookup error: undefined symbol: bam_mods_at_qpos

Issue - State: closed - Opened by szakallasn3 over 1 year ago - 2 comments

#51 - ML tag can’t show the correct skipped sites number in Nanopore sequencing

Issue - State: closed - Opened by PanZiwei over 1 year ago - 1 comment

#50 - Unexpected behavior calling `list()` on `ModBam().reads()` generator

Issue - State: closed - Opened by thekugelmeister over 1 year ago - 5 comments

#49 - error while loading shared libraries: libhts.so.3

Issue - State: closed - Opened by palakela over 1 year ago - 2 comments

#48 - Don't have reference fasta

Issue - State: closed - Opened by keenhl almost 2 years ago - 6 comments

#47 - No modified base tags for reads with supplementary alignments?

Issue - State: closed - Opened by PanZiwei almost 2 years ago - 12 comments

#46 - Working with Dorado Basecaller

Issue - State: closed - Opened by ethan-mcq almost 2 years ago - 1 comment

#45 - `modbampy.ModBam.pileup` idiosyncrasies or inconsistencies

Issue - State: closed - Opened by thekugelmeister almost 2 years ago - 4 comments

#44 - How to get mapped sites number from modbam file

Issue - State: closed - Opened by PanZiwei almost 2 years ago - 1 comment

#43 - Question about HG002 data

Issue - State: closed - Opened by PanZiwei almost 2 years ago - 1 comment

#42 - ModuleNotFoundError: No module named 'libmodbampy'

Issue - State: closed - Opened by rowanhowellGE almost 2 years ago - 4 comments

#41 - Output Issues

Issue - State: closed - Opened by jchan3188 almost 2 years ago - 2 comments

#40 - Dead link

Issue - State: closed - Opened by Shians almost 2 years ago - 1 comment

#39 - Using CRAM files is very slow (10x slower) if REF_CACHE is not configured beforehand

Issue - State: closed - Opened by Coppini almost 2 years ago - 5 comments

#38 - Install modbam2bed via anaconda

Issue - State: closed - Opened by ekushele almost 2 years ago - 3 comments

#37 - about CpG number in modbam2bed output

Issue - State: closed - Opened by kaanokay almost 2 years ago - 2 comments

#36 - "make modbam2bed" fails

Issue - State: closed - Opened by ekushele almost 2 years ago - 3 comments

#35 - `modbam2bed` with or without `--aggregate`?

Issue - State: closed - Opened by PanZiwei about 2 years ago - 1 comment

#34 - [E::fai_retrieve] Failed to retrieve block: unexpected end of file

Issue - State: closed - Opened by PanZiwei about 2 years ago - 6 comments

#33 - pip install fails on MacOS

Issue - State: closed - Opened by marcpaga about 2 years ago - 3 comments

#32 - How to interpret 0-255 methylation score

Issue - State: closed - Opened by marcpaga about 2 years ago - 2 comments

#31 - how to deal with many bam files

Issue - State: closed - Opened by Aline-Git about 2 years ago - 2 comments

#30 - How to modified the value in pos_mod

Issue - State: closed - Opened by JeremyQuo about 2 years ago - 3 comments

#29 - How to covert a bedMthy to modbam?

Issue - State: closed - Opened by JeremyQuo about 2 years ago - 1 comment

#28 - CIGAR and query sequence lengths differ for

Issue - State: closed - Opened by charliechen912ilovbash about 2 years ago - 3 comments

#27 - what is the difference between acc.bed and .bed file?

Issue - State: closed - Opened by AlineMuyle about 2 years ago - 2 comments

#26 - No output

Issue - State: closed - Opened by charliechen912ilovbash about 2 years ago - 2 comments

#24 - unaligned bam

Issue - State: closed - Opened by rrazaghi over 2 years ago - 5 comments

#23 - error when installing via conda

Issue - State: closed - Opened by Jane-Gibson over 2 years ago - 2 comments

#22 - Fix project URL on PyPI

Pull Request - State: closed - Opened by alexomics over 2 years ago

#21 - Hi cjw85,

Issue - State: closed - Opened by cjw85 over 2 years ago - 1 comment

#20 - More choices for modified base calls (feature request)

Issue - State: closed - Opened by sathish-t over 2 years ago - 7 comments

#19 - -b, --mod_threshold

Issue - State: closed - Opened by carolinehey over 2 years ago - 1 comment

#18 - Does modbam2bed handle soft clips?

Issue - State: closed - Opened by billytcl over 2 years ago - 3 comments

#17 - Adding motif context to modbampy

Issue - State: closed - Opened by rrazaghi over 2 years ago - 2 comments

#16 - "-1" positions in output using modbampy

Issue - State: closed - Opened by pterzian over 2 years ago - 2 comments

#15 - Failed to find reference sequence 'contig_1' in bam.

Issue - State: closed - Opened by Kirk3gaard over 2 years ago - 6 comments

#14 - Weird output parsing HG002 ont bonito-remora data

Issue - State: closed - Opened by rrazaghi over 2 years ago - 1 comment

#13 - Passing multiple sorted bamfiles VS one sorted and merged bamfile to modbam2bed

Issue - State: closed - Opened by TeiturAK over 2 years ago - 5 comments

#12 - Does modbam2bed require a sorted bam file?

Issue - State: closed - Opened by billytcl over 2 years ago - 1 comment

#11 - the coverage we really want is N_mod+N_canon

Issue - State: closed - Opened by benbfly over 2 years ago - 4 comments

#10 - Strange results with a very high coverage

Issue - State: closed - Opened by e-sollier over 2 years ago - 4 comments

#9 - More sequence contexts for modified base calls (feature request)

Issue - State: closed - Opened by TeiturAK over 2 years ago - 12 comments

#8 - No module named libmodbampy

Issue - State: closed - Opened by HJeffery over 2 years ago - 4 comments

#7 - Column 5 score seems wrong

Issue - State: closed - Opened by benbfly almost 3 years ago - 1 comment

#6 - Feature request - outfile

Issue - State: closed - Opened by colindaven almost 3 years ago - 2 comments

#5 - typos

Pull Request - State: closed - Opened by colindaven almost 3 years ago

#4 - modbam2bed biowasm per read output

Issue - State: closed - Opened by rrazaghi almost 3 years ago - 2 comments

#3 - add core alignment information to modbampy

Issue - State: closed - Opened by rrazaghi almost 3 years ago - 16 comments

#2 - Any way to get this to output per read mods in a bam file like megalodon?

Issue - State: closed - Opened by billytcl almost 3 years ago - 10 comments

#1 - copping segfault :/

Issue - State: closed - Opened by serine over 3 years ago - 10 comments