Ecosyste.ms: Issues

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

GitHub / iprada/Circle-Map issues and pull requests

#103 - OSError: AF_UNIX path too long

Issue - State: open - Opened by newpest 27 days ago - 5 comments

#102 - CRAM support

Issue - State: closed - Opened by talhamufeed 2 months ago - 6 comments

#101 - fixed small bugs

Pull Request - State: open - Opened by cchd0001 3 months ago - 1 comment

#100 - ignore unparsed_pd is empty

Issue - State: open - Opened by newpest 3 months ago

#99 - Bio.Alphabet has been removed from Biopython

Issue - State: closed - Opened by newpest 3 months ago

#98 - RuntimeWarning in Circle-Map Realign

Issue - State: open - Opened by hanssli 6 months ago - 3 comments

#97 - A problem of searching principle of Circle-Map

Issue - State: open - Opened by FeiLiuEM about 1 year ago - 3 comments

#96 - Circle-map Realign run too slow at the end.

Issue - State: open - Opened by Chester729 about 1 year ago

#95 - input data

Issue - State: open - Opened by CaroleBelliardo about 1 year ago - 1 comment

#94 - complicated circles

Issue - State: open - Opened by natashaweiser over 1 year ago

#93 - some errors report about Circle-Map Repeats -i

Issue - State: open - Opened by fanch1122 over 1 year ago

#92 - Circle Map Realign

Issue - State: open - Opened by uretaj over 1 year ago

#91 - Circle-Map Repeats output file

Issue - State: open - Opened by simonestensgaard over 1 year ago - 2 comments

#90 - How to plot the results in circular form?

Issue - State: open - Opened by ShixiangWang over 1 year ago

#89 - can I split alignment by chromosomes to speed up the last step

Issue - State: open - Opened by zhuyiqin almost 2 years ago

#88 - Using bowtie2 with circle-map

Issue - State: open - Opened by nguyenkduy0510 almost 2 years ago

#87 - ImportError: Bio.Alphabet has been removed from Biopython.

Issue - State: closed - Opened by ZHONGHONGXIN about 2 years ago

#86 - Circle_Map takes an unusually long time to read files.

Issue - State: open - Opened by ghost about 2 years ago - 1 comment

#85 - Could Circle-Map detect chimeric eccDNAs?

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

#84 - Update Pypi Version to 1.1.5

Issue - State: open - Opened by DSchreyer about 2 years ago

#83 - glibc conflicts when installing

Issue - State: closed - Opened by zhuyiqin over 2 years ago

#82 - [#75] ReadExtractor support absolute path

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

#81 - Why do the coordinates of the circle exceed the length of the contig？

Issue - State: open - Opened by xdli009 over 2 years ago - 1 comment

#80 - Questions about Circle-Map bam2bam

Issue - State: open - Opened by 178875 over 2 years ago

#79 - cannot convert float NaN to integer

Issue - State: open - Opened by lssb over 2 years ago

#78 - how to avoid to getting repeat region ?

Issue - State: open - Opened by panxiaoguang over 2 years ago - 1 comment

#77 - The output files of Circle Map Repeats

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

#76 - questions about quantification

Issue - State: open - Opened by taoshengqiansui almost 3 years ago - 2 comments

#75 - cannot use absolute path in ReadExtractor

Issue - State: open - Opened by jinyung almost 3 years ago - 1 comment

#74 - Problems with 'Split reads' and' Discordants reads'

Issue - State: closed - Opened by Leo152 almost 3 years ago - 2 comments

#73 - Question regarding the "Circle score"

Issue - State: closed - Opened by ko0000 almost 3 years ago - 3 comments

#72 - Questions about the Circle-map ReadExtractor

Issue - State: open - Opened by Le1223 almost 3 years ago - 6 comments

#68 - Could not retrieve index file for examples

Issue - State: closed - Opened by ShixiangWang about 3 years ago - 6 comments

#67 - Criteria for filtering

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

#66 - Long runtime with Circle Realign?

Issue - State: open - Opened by hartlama over 3 years ago - 5 comments

#65 - Realign KeyError

Issue - State: closed - Opened by hartlama over 3 years ago - 9 comments

#64 - Fail to open alignment file

Issue - State: closed - Opened by hartlama over 3 years ago

#63 - ecDNA only from Chr10 and Chr11

Issue - State: open - Opened by lanliting over 3 years ago - 4 comments

#62 - ecDNA detected only in Chr10 and Chr11

Issue - State: closed - Opened by lanliting over 3 years ago

#61 - Only got ec

Issue - State: closed - Opened by lanliting over 3 years ago

#60 - combining samples before Circle-Map analysis

Issue - State: closed - Opened by hartlama over 3 years ago - 5 comments

#59 - Some columns in the output have no values

Issue - State: open - Opened by Somnvs over 3 years ago - 2 comments

#58 - NotImplementedError: "sortBed"

Issue - State: closed - Opened by yjx1217 over 3 years ago - 3 comments

#57 - Some doubts about the output of Circle-map

Issue - State: open - Opened by Somnvs almost 4 years ago - 1 comment

#56 - Preprocessing circle-seq data before using circle-map

Issue - State: open - Opened by Jiangxiaoyu1i almost 4 years ago - 1 comment

#55 - ReadExtractor fails if the first read in bam file is an unpaired read2

Issue - State: open - Opened by johnstonmj almost 4 years ago - 1 comment

#54 - about samtools index for bam

Issue - State: open - Opened by caijingtao1993 almost 4 years ago - 4 comments

#53 - Command help

Issue - State: closed - Opened by gq97 almost 4 years ago - 2 comments

#52 - An error happenend during execution. Exiting

Issue - State: open - Opened by johnstonmj almost 4 years ago - 9 comments

#51 - Divide by zero during coverage calculation?

Issue - State: open - Opened by johnstonmj almost 4 years ago

#50 - Warnings in Circle-Map Realign tutorial

Issue - State: open - Opened by johnstonmj about 4 years ago - 5 comments

#49 - ImportError: Bio.Alphabet has been removed from Biopython.

Issue - State: closed - Opened by shaka-emperor about 4 years ago - 7 comments

#48 - Question: Tutorial step 2 skip orientation FF/RF/RR by bwa mem

Issue - State: closed - Opened by shaka-emperor about 4 years ago - 5 comments

#47 - Latest biopython version breaks Alphabet dependency

Issue - State: open - Opened by johnstonmj about 4 years ago - 9 comments

#46 - UserWarning: Failed on interval chrom

Issue - State: open - Opened by xdli009 about 4 years ago - 1 comment

#45 - Questions of Circle-Map Repeats and Realignment

Issue - State: open - Opened by Bio-MingChen about 4 years ago - 1 comment

#44 - Sequence extraction of spite reads and discordants reads

Issue - State: open - Opened by caijingtao1993 about 4 years ago - 5 comments

#43 - Would circle-map works for Nanopore reads?

Issue - State: open - Opened by WeijiaSu about 4 years ago - 1 comment

#42 - how to use Circle-map to get counts for a specific ecDNA?

Issue - State: closed - Opened by shaka-emperor about 4 years ago - 10 comments

#41 - Is the classic WGS data well compatible with circle-seq

Issue - State: open - Opened by zhang616123 about 4 years ago - 5 comments

#40 - NGmerge or fastqc shoud be used in quality control before alignment

Issue - State: open - Opened by pangxueyu233 about 4 years ago - 7 comments

#39 - how to get ecc reads from Circle-map outputs file

Issue - State: closed - Opened by panxiaoguang about 4 years ago - 3 comments

#38 - Connection refused while downloading the raw data

Issue - State: closed - Opened by gq97 about 4 years ago - 2 comments

#37 - About Circle-Map Realign calculation

Issue - State: open - Opened by caijingtao1993 over 4 years ago - 12 comments

#35 - How to speed up the last step of Circle-Map Realign?

Issue - State: open - Opened by junchend over 4 years ago - 10 comments

#34 - WARNING: Could not compute the probability for the mate interval priors

Issue - State: open - Opened by zhang919 over 4 years ago - 11 comments

#33 - AttributeError: 'int' object has no attribute 'is_integer'

Issue - State: closed - Opened by poflawless over 4 years ago - 3 comments
Labels: question

#32 - Does circle-map work well if ecdna contains structural variation?

Issue - State: closed - Opened by zhang919 over 4 years ago - 3 comments
Labels: question

#31 - Suspicious feedback during coverage computation

Issue - State: closed - Opened by tchrisboles over 4 years ago - 2 comments
Labels: question

#30 - a question

Issue - State: closed - Opened by tchrisboles over 4 years ago - 3 comments
Labels: question

#29 - Interpreting runtime warnings

Issue - State: closed - Opened by diplockn over 4 years ago - 1 comment
Labels: question

#28 - OSError: [Errno 28] No space left on device

Issue - State: open - Opened by diplockn over 4 years ago - 4 comments
Labels: bug

#27 - Realign process running at very low CPU Usage

Issue - State: closed - Opened by huangyizR over 4 years ago - 5 comments
Labels: bug, duplicate, question

#26 - bwa not work

Issue - State: closed - Opened by Chuan0518 almost 5 years ago - 3 comments
Labels: bug

#25 - Error on coverage calculation of Circle-Map Repeats

Issue - State: closed - Opened by iprada about 5 years ago
Labels: bug

#24 - Circle-Map does not install properly

Issue - State: closed - Opened by Ananthu3898 about 5 years ago - 2 comments
Labels: invalid

#23 - How does Circle-Map use hard clipped reads?

Issue - State: closed - Opened by tchrisboles about 5 years ago - 1 comment
Labels: enhancement, question

#22 - Segmental duplications give false circle signals?

Issue - State: closed - Opened by tchrisboles about 5 years ago - 2 comments
Labels: enhancement

#21 - Realign process seems to freeze

Issue - State: closed - Opened by tchrisboles about 5 years ago - 5 comments
Labels: enhancement

#19 - Circle-Map Output File

Issue - State: closed - Opened by Abdubidopsis about 5 years ago - 6 comments
Labels: question

#18 - Circle-Map takes longer on server

Issue - State: closed - Opened by Abdubidopsis about 5 years ago - 5 comments
Labels: question

#17 - Use classifiers to specify the license.

Pull Request - State: closed - Opened by Steap over 5 years ago - 1 comment

#16 - Create LICENSE

Pull Request - State: closed - Opened by iprada over 5 years ago