Ecosyste.ms: Issues

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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

#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

#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

#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

#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

#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