Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / bedops/bedops issues and pull requests
#284 - starch/unstarch produces error when --gzip compression is applied to empty (0-byte) bed file
Issue -
State: closed - Opened by bgulko 10 months ago
- 2 comments
Labels: bug, question
#283 - Weird result on a specific file
Issue -
State: closed - Opened by pdeven 10 months ago
- 4 comments
Labels: bug, question
#282 - How to use `bedops --intersect` operation to write all the columns into output BED files?
Issue -
State: closed - Opened by jjiang92292 10 months ago
- 2 comments
#281 - sam2bed fails to split some sam entries correctly
Issue -
State: closed - Opened by malyshev-andrey about 1 year ago
- 1 comment
Labels: bug, question
#280 - bedmap issue
Issue -
State: closed - Opened by PyunJung-Min about 1 year ago
- 1 comment
#279 - vcf2bed; Segmentation fault
Issue -
State: closed - Opened by PyunJung-Min about 1 year ago
- 1 comment
#278 - interpret output of infer_experiment.py
Issue -
State: closed - Opened by lalalagartija over 1 year ago
- 2 comments
#277 - Segmentation fault (core dumped)
Issue -
State: closed - Opened by priyambial123 over 1 year ago
- 6 comments
#276 - Semicolon in 'gene_name' or 'transcript_name' breaks gtf2bed
Issue -
State: closed - Opened by NanoCoreUSA over 1 year ago
- 2 comments
#275 - gff2bed fails with "Non-numeric start coordinate. "
Issue -
State: closed - Opened by shbrainard almost 2 years ago
- 4 comments
Labels: bug, question
#274 - *** Error in `convert2bed': realloc(): invalid next size: 0x00005639369afba0 ***
Issue -
State: closed - Opened by aalkin2001 almost 2 years ago
- 1 comment
Labels: question
#273 - "Error: Invalid WIG line" when using convert2bed on wiggle file
Issue -
State: closed - Opened by eggrandio about 2 years ago
- 3 comments
Labels: question
#272 - unstarch --verify-signature fails on some files with header
Issue -
State: open - Opened by vulpescu about 2 years ago
- 1 comment
Labels: bug, question
#271 - Bedmap fails with gzipped starch archives
Issue -
State: open - Opened by vulpescu over 2 years ago
#270 - Possible issue with `--no-overlaps` option in `closest-features`
Issue -
State: closed - Opened by alexpreynolds over 2 years ago
- 3 comments
Labels: bug, question
#269 - Add 2.4.40 to bioconda?
Issue -
State: closed - Opened by russellsmithies over 2 years ago
- 4 comments
Labels: feature request
#268 - bam2bed leaves the CIGAR string untouched
Issue -
State: closed - Opened by LalitNM over 2 years ago
- 1 comment
Labels: bug, question, feature request
#267 - Build failures due to template const member functions updating object fields
Issue -
State: closed - Opened by jmarshall over 2 years ago
- 3 comments
Labels: question
#266 - Document performance of `bedextract`
Issue -
State: closed - Opened by alexlenail over 2 years ago
- 6 comments
#265 - Error: SortDetails.cpp, 885: Unable to create BED structure.
Issue -
State: closed - Opened by alexlenail over 2 years ago
- 7 comments
Labels: bug, question
#264 - `bedops -u *.bed | bedmap --max-element` does not select max element
Issue -
State: closed - Opened by alexlenail over 2 years ago
- 6 comments
#263 - Mysterious error in bedops -u
Issue -
State: closed - Opened by alexlenail over 2 years ago
- 3 comments
#262 - Version 2.4.40 changed after release
Issue -
State: closed - Opened by amadejpapez about 3 years ago
- 2 comments
#261 - error in vcf2bed
Issue -
State: closed - Opened by ghost about 3 years ago
- 11 comments
#260 - BEDOPS v2.4.40 linux .tar.bz2 release
Issue -
State: closed - Opened by epaule over 3 years ago
- 1 comment
Labels: bug
#259 - Document which fields sort-bed --unique filters BED elements by all fields, or only some fields.
Issue -
State: closed - Opened by alexlenail over 3 years ago
- 1 comment
#258 - Should bedops sort-bed really fail if the start and end position are the same?
Issue -
State: closed - Opened by alexlenail over 3 years ago
- 2 comments
#257 - Investigate order of application of `--ec` with `--chrom` in `bedops`
Issue -
State: open - Opened by alexpreynolds over 3 years ago
Labels: bug, enhancement, question, feature request
#256 - Modify behavior when wig2bed `--multisplit` option has no <val> specified
Issue -
State: closed - Opened by alexpreynolds over 3 years ago
- 1 comment
Labels: bug, enhancement
#255 - BED file is empty after running wig2bed on WigFix overnight, had to terminate
Issue -
State: closed - Opened by RohanParikh00 over 3 years ago
- 8 comments
Labels: enhancement
#254 - bedmap uses >150GB ram on an input file of 10GB
Issue -
State: closed - Opened by yonniejon over 3 years ago
- 8 comments
#253 - Remove requirement for chromosome name prefix in `wig2bed`
Issue -
State: closed - Opened by alexpreynolds over 3 years ago
- 1 comment
Labels: bug, enhancement
#252 - BLha blah abl
Issue -
State: closed - Opened by alexpreynolds over 3 years ago
- 1 comment
#251 - issue with bedops --merge
Issue -
State: closed - Opened by MarjorieRoskes over 3 years ago
- 2 comments
#250 - Investigate having `--min`/`--max`/etc. operators support `--echo-*` with `--prec N`
Issue -
State: open - Opened by alexpreynolds over 3 years ago
Labels: enhancement, question, feature request
#249 - bedops breaks with >1000 files
Issue -
State: closed - Opened by stevekm almost 4 years ago
- 3 comments
#248 - Problem with starch
Issue -
State: closed - Opened by cadley-nyulangone almost 4 years ago
- 3 comments
Labels: question
#247 - Does not find convert2bed binary file in /bedops/bin directory
Issue -
State: closed - Opened by yangyxt almost 4 years ago
- 1 comment
#246 - rmsk2bed Creates Non-Compliant BED File
Issue -
State: closed - Opened by DarioS almost 4 years ago
- 2 comments
Labels: bug, question
#245 - bedextract doesn't work
Issue -
State: closed - Opened by PanZiwei about 4 years ago
- 1 comment
Labels: question
#244 - gff2bed doesn't place gene id values into 4th BED column
Issue -
State: closed - Opened by mmokrejs about 4 years ago
- 2 comments
Labels: question, documentation
#243 - gtf2bed from bedops-2.4.39: Error: Potentially missing gene or transcript ID from GTF attributes (malformed GTF at line [1]?)
Issue -
State: closed - Opened by mmokrejs about 4 years ago
- 5 comments
#242 - Makefiles do not respect users CXXFLAGS
Issue -
State: closed - Opened by mmokrejs about 4 years ago
- 4 comments
Labels: feature request
#241 - bedmap error message does not reflect the reason for failure
Issue -
State: closed - Opened by aminards about 4 years ago
- 1 comment
#240 - gtf2bed example doesn't work
Issue -
State: closed - Opened by vreuter about 4 years ago
- 7 comments
Labels: question
#239 - Error: Invalid wig ID on line 1
Issue -
State: closed - Opened by ghost over 4 years ago
- 10 comments
Labels: enhancement, feature request
#238 - wigToBed fails with Error: Invalid wig ID on line 2
Issue -
State: closed - Opened by LeilyR over 4 years ago
- 1 comment
#237 - Start coordinate is too large - vcftobed conversion
Issue -
State: closed - Opened by asmariyaz23 over 4 years ago
- 3 comments
Labels: question
#236 - Modify sort-bed options or help statement
Issue -
State: closed - Opened by alexpreynolds over 4 years ago
- 1 comment
Labels: bug, enhancement, documentation
#235 - segfaults from convert2bed
Issue -
State: closed - Opened by diekhans over 4 years ago
- 4 comments
Labels: bug
#234 - Is there a way to omit compression timestamp when starching?
Issue -
State: closed - Opened by ottojolanki over 4 years ago
- 2 comments
#232 - bedmap count incorrect result
Issue -
State: closed - Opened by skytguuu almost 5 years ago
- 3 comments
#231 - sam2bed output fault
Issue -
State: closed - Opened by arnavgupta06754 almost 5 years ago
- 7 comments
#230 - vcf2bed failed with "Error: Could not find newline in intermediate buffer; check input [11821 | 29288 | 41109]"
Issue -
State: closed - Opened by yunhailuo about 5 years ago
- 12 comments
#229 - fix for bedmap --header produces no output
Pull Request -
State: closed - Opened by andremrsantos about 5 years ago
- 7 comments
#228 - bedextract efficiency problem
Issue -
State: closed - Opened by sjneph over 5 years ago
- 1 comment
Labels: enhancement
#227 - Invalid WIG line when using wig2bed on wig obtained using bigWigToWig
Issue -
State: closed - Opened by blaiseli over 5 years ago
- 2 comments
Labels: question
#226 - Problem that needs solution
Issue -
State: closed - Opened by demis001 over 5 years ago
- 6 comments
#225 - feature-request - gtf2bed: on failure, output help to stderr
Issue -
State: closed - Opened by russHyde over 5 years ago
- 3 comments
#224 - bedops readthedocs index page image links seem to be broken
Issue -
State: closed - Opened by udincer over 5 years ago
- 2 comments
#223 - Starchcat segfault?
Issue -
State: closed - Opened by alexpreynolds over 5 years ago
- 1 comment
Labels: bug, question
#222 - bedextract segmentation fault when operating on Agilent SureSelect v4+UTR regions file
Issue -
State: closed - Opened by khughitt over 5 years ago
- 2 comments
#221 - problem with compile finding standard c libraries
Issue -
State: closed - Opened by mforde84 over 5 years ago
- 1 comment
#220 - bedmap --header produces no output
Issue -
State: closed - Opened by vulpescu over 5 years ago
- 5 comments
#219 - --prec does not affect reference file score column when run as bedmap [ref file]
Issue -
State: open - Opened by mattmaurano over 5 years ago
- 2 comments
Labels: bug
#218 - vcf2bed and deletions
Issue -
State: closed - Opened by nathanhaigh over 5 years ago
- 10 comments
Labels: bug, question
#217 - Multiple crashes when using convert2bed
Issue -
State: closed - Opened by hongxuchen almost 6 years ago
- 2 comments
Labels: question
#216 - Merge only overlapping regions
Issue -
State: closed - Opened by nandankita almost 6 years ago
- 6 comments
#215 - `POS + length(CIGAR) - 1` should be `POS + length(SEQ) - 1`
Issue -
State: closed - Opened by dongzhuoer almost 6 years ago
- 3 comments
Labels: bug, question, documentation
#214 - Add support for merging GZIP (or BGZIP) BED files
Issue -
State: closed - Opened by fgvieira almost 6 years ago
- 1 comment
#213 - Count gave me weird result
Issue -
State: open - Opened by demis001 almost 6 years ago
- 6 comments
Labels: feature request
#212 - bedops --intersect outputs empty file when input contains comments
Issue -
State: closed - Opened by rioualen about 6 years ago
- 2 comments
#211 - bedmap (bedops) will consider strand? and bed12 (blocked) files supported?
Issue -
State: closed - Opened by Linhua-Sun about 6 years ago
- 2 comments
#210 - Floating point exception
Issue -
State: closed - Opened by brianpenghe about 6 years ago
- 6 comments
#209 - Unstarch `--is-starch` option should only check small portion of input file
Issue -
State: closed - Opened by alexpreynolds about 6 years ago
- 1 comment
Labels: bug, enhancement
#208 - convert2bed-megarow fails with "Could not find newline" when given very large SAM files
Issue -
State: closed - Opened by SchwarzEM over 6 years ago
- 13 comments
Labels: enhancement, question, feature request
#207 - convert2bed-megarow has persistent "Segmentation fault" error
Issue -
State: closed - Opened by SchwarzEM over 6 years ago
- 5 comments
Labels: bug, question
#206 - [Feature Request]: --echo-max-map-score
Issue -
State: closed - Opened by alexlenail over 6 years ago
- 1 comment
#205 - [Feature Request]: Option to select specific column in bedmap
Issue -
State: open - Opened by alexlenail over 6 years ago
- 2 comments
#204 - GTF to bed chromosome coordination change
Issue -
State: closed - Opened by xinl22 almost 7 years ago
- 3 comments
Labels: question
#203 - intersection between two files with percentage
Issue -
State: closed - Opened by gk7279 almost 7 years ago
- 3 comments
#202 - Homebrew installation change
Issue -
State: closed - Opened by EricFromCanada almost 7 years ago
- 1 comment
#201 - comapre two bam files based on read ID
Issue -
State: closed - Opened by gk7279 almost 7 years ago
- 1 comment
#200 - bedops hangs if passed a directory
Issue -
State: open - Opened by sjneph about 7 years ago
Labels: bug, enhancement
#199 - nest checking happening in non-fast mode
Issue -
State: closed - Opened by sjneph about 7 years ago
- 1 comment
Labels: bug
#198 - Is there a way to report bedmap results in order of IDs or filenames?
Issue -
State: closed - Opened by alexpreynolds about 7 years ago
- 5 comments
Labels: bug, question
#197 - change behavior of unstarch --is-starch
Issue -
State: closed - Opened by sjneph about 7 years ago
- 1 comment
Labels: feature request
#196 - Consider adding `-u` and `-d` options to `sort-bed` to print unique and duplicated elements
Issue -
State: closed - Opened by alexpreynolds about 7 years ago
- 9 comments
Labels: enhancement, question, feature request
#195 - Issue with ID string length when starch-ing
Issue -
State: closed - Opened by alexpreynolds about 7 years ago
- 1 comment
Labels: bug, question
#194 - debug target fails
Issue -
State: closed - Opened by alexpreynolds about 7 years ago
Labels: bug, question
#193 - bedmap --exact problematic with --ec
Issue -
State: closed - Opened by sjneph about 7 years ago
- 1 comment
Labels: bug
#192 - Converting WIG to BED file
Issue -
State: closed - Opened by claudiadast about 7 years ago
- 3 comments
Labels: question
#191 - --wmean not working
Issue -
State: closed - Opened by brightgreendot over 7 years ago
- 3 comments
Labels: bug
#190 - bed to value
Issue -
State: closed - Opened by gk7279 over 7 years ago
- 7 comments
Labels: question
#189 - closest-features to report upsteam/downstream features only
Issue -
State: closed - Opened by isthisthat over 7 years ago
- 8 comments
Labels: feature request
#188 - BEDOPS.2.4.27.pkg contains broken symbolic links
Issue -
State: closed - Opened by rsharris over 7 years ago
- 4 comments
Labels: bug, question
#186 - Adding a license to a repository
Issue -
State: closed - Opened by tmozgach over 7 years ago
- 2 comments
#174 - Potential bugs to investigate
Issue -
State: closed - Opened by alexpreynolds almost 8 years ago
- 20 comments
Labels: bug, question
#159 - Uninstallation of the Bedops
Issue -
State: closed - Opened by mortunco about 8 years ago
- 3 comments
Labels: enhancement, feature request
#157 - Support for an arbitrary number of CIGAR ops (was: convert2bed can't find sort-bed binary)
Issue -
State: closed - Opened by adamfreedman over 8 years ago
- 34 comments
Labels: bug, question