Ecosyste.ms: Issues

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

GitHub / genome/bam-readcount issues and pull requests

#105 - Questionably long runtime for RNA BAMs vs. DNA BAMs?

Issue - State: closed - Opened by seetarajpara over 1 year ago

#104 - Interpretation of indels

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

#103 - read depth incorrect

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

#102 - Compilation Issue

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

#101 - Reported depth not matching

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

#100 - Issue on installation

Issue - State: open - Opened by idoit4fun over 2 years ago

#99 - fatal error: compilation failed

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

#98 - Identify reads aligned to mutant and wild type sequences

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

#97 - Badge

Pull Request - State: closed - Opened by sridhar0605 almost 3 years ago

#95 - Unix conv help message edits

Pull Request - State: closed - Opened by sridhar0605 almost 3 years ago

#94 - help message edits

Pull Request - State: closed - Opened by sridhar0605 almost 3 years ago

#93 - Version and Author contri patch

Pull Request - State: closed - Opened by sridhar0605 almost 3 years ago

#92 - how to get the site list for indels?

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

#91 - Add tutorial

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

#90 - how to get a region file

Issue - State: closed - Opened by stroke1989 about 3 years ago - 3 comments

#89 - Support for BAM CSI index

Issue - State: closed - Opened by f-huber about 3 years ago - 1 comment

#88 - Error when path_to_bam have bam in middle

Issue - State: open - Opened by sssimonyang about 3 years ago

#87 - Inconsistent output

Issue - State: open - Opened by mnshgl0110 about 3 years ago - 2 comments

#86 - WARNING

Issue - State: closed - Opened by stroke1989 about 3 years ago - 3 comments

#85 - Reason for low coverage output for deepseq data

Issue - State: open - Opened by YashaNazirB about 3 years ago - 5 comments

#84 - [JOSS REVIEW] Any functionality documentation?

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

#83 - [JOSS REVIEW] Missing the community contribution guidelines

Issue - State: closed - Opened by bebatut about 3 years ago - 2 comments
Labels: joss-review-finished

#82 - [JOSS REVIEW] minor edits to the manuscript

Issue - State: closed - Opened by friedue about 3 years ago - 3 comments
Labels: joss-review-finished

#81 - [JOSS REVIEW] Minor edits to the github-based documentation

Issue - State: open - Opened by friedue about 3 years ago - 2 comments

#80 - [JOSS REVIEW] Example usage

Issue - State: closed - Opened by friedue about 3 years ago - 6 comments
Labels: joss-review-finished

#79 - [JOSS REVIEW] docker documentation

Issue - State: closed - Opened by friedue about 3 years ago - 3 comments
Labels: joss-review-finished

#78 - compilation failed

Issue - State: open - Opened by lmanchon about 3 years ago - 5 comments

#77 - Make Error for boost on MacOS

Issue - State: open - Opened by chintan-vora-tfs over 3 years ago - 4 comments

#76 - Move Docker docs to top of README

Pull Request - State: closed - Opened by apldx over 3 years ago

#75 - Compilation fails because of missing -fPIC

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

#74 - Add Docker and clean up

Pull Request - State: closed - Opened by apldx over 3 years ago

#73 - Samtools 1.10

Pull Request - State: closed - Opened by seqfu over 3 years ago - 1 comment

#71 - fpfilter.pl - failed to get readcounts for variant allele

Issue - State: open - Opened by Souzavgp over 3 years ago

#70 - Fail to open BAM file –q

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

#69 - Max depth 8000

Issue - State: closed - Opened by LauraVP1994 almost 4 years ago - 1 comment

#68 - Getting the read names/ IDs?

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

#67 - Distance to both 5' and 3' ends

Issue - State: open - Opened by matnguyen over 4 years ago

#66 - Is there a recommended citation for this tool?

Issue - State: closed - Opened by whtns about 5 years ago - 1 comment

#65 - Update included samtools and boost

Issue - State: open - Opened by serge2016 about 5 years ago - 3 comments

#64 - Run without errors but failed to produce the site list

Issue - State: open - Opened by drtamermansour about 5 years ago - 8 comments

#63 - missing avg_distance_to_effective_3p_end

Issue - State: open - Opened by stemangiola over 5 years ago

#62 - Feature request: Request for unmapped region option

Issue - State: open - Opened by ankit4035 over 5 years ago - 2 comments

#61 - fail to load bam index

Issue - State: closed - Opened by mcfog1 over 5 years ago

#60 - make test fails RunBamReadcount (python vs python2)

Issue - State: open - Opened by darked89 over 5 years ago

#59 - Update bioconda deployment to Python3.7

Issue - State: open - Opened by MatthewPorterGN almost 6 years ago - 2 comments

#58 - print-individual-mapq not working

Issue - State: open - Opened by fkokocinski about 6 years ago - 2 comments

#57 - a question of how to use bam-readcount on insertions?

Issue - State: closed - Opened by rayliu0115 over 6 years ago - 1 comment

#56 - [bam_plp_destroy] memory leak: 1. Continue anyway.

Issue - State: open - Opened by jflucier over 6 years ago - 1 comment

#54 - Deletion counts behaviour

Issue - State: closed - Opened by iranmdl over 6 years ago - 3 comments

#53 - Update max_warnings to 10

Pull Request - State: closed - Opened by colindaven almost 7 years ago

#52 - List of base pair quality

Issue - State: open - Opened by aziouez25 almost 7 years ago

#51 - read count limit 8000

Issue - State: closed - Opened by snuernberg almost 7 years ago - 3 comments

#50 - index not found for gatk output

Issue - State: open - Opened by crazyhottommy almost 7 years ago - 1 comment

#49 - Problem on Intallaion of bam_readcount

Issue - State: open - Opened by bioinfo-dirty-jobs almost 7 years ago

#48 - speed improvements

Issue - State: open - Opened by duartemolha almost 7 years ago - 1 comment

#47 - no output when running with -l varscan data

Issue - State: closed - Opened by splaisan about 7 years ago - 1 comment

#46 - are soft-clipped bases counted for the depth?

Issue - State: closed - Opened by iranmdl about 7 years ago - 7 comments

#45 - Filteriing paired end data

Issue - State: closed - Opened by ktroule about 7 years ago - 2 comments

#44 - --site-list option is not working

Issue - State: open - Opened by ycl6 over 7 years ago - 4 comments

#42 - detailed format to calculate "avg_sum_mismatch_qualities" ?

Issue - State: open - Opened by zeronot over 7 years ago - 1 comment

#41 - make error

Issue - State: open - Opened by fwks over 7 years ago - 1 comment

#40 - Different alignment of indels in DNA and RNA

Issue - State: closed - Opened by nilsrudqvist over 7 years ago - 6 comments

#39 - CIGAR error

Issue - State: closed - Opened by avilella over 7 years ago - 1 comment

#38 - Improve per library documentation

Pull Request - State: closed - Opened by bainscou over 7 years ago

#37 - min-base-quality not giving expected output (also on biostars)

Issue - State: open - Opened by sheenamt almost 8 years ago - 2 comments

#36 - Non -ACGTN counts

Issue - State: open - Opened by iranmdl almost 8 years ago - 7 comments

#35 - compiling error

Issue - State: open - Opened by kaji331 almost 8 years ago - 1 comment

#34 - bam-readcount

Issue - State: open - Opened by xiezhan about 8 years ago - 1 comment

#33 - Is it possible to output read count based on strandness

Issue - State: closed - Opened by crazyhottommy about 8 years ago

#32 - Compilation error with abs function in BasicStat.cpp

Issue - State: closed - Opened by germelcar about 8 years ago - 1 comment

#31 - Fix segmentation fault when BAM file does not exist

Pull Request - State: closed - Opened by sambrightman over 8 years ago - 2 comments

#30 - Running without a region doesn't work

Issue - State: open - Opened by ernfrid over 8 years ago - 4 comments

#29 - bam-readcount

Issue - State: closed - Opened by huiyu3892 over 8 years ago - 1 comment

#28 - Missing LICENSE file

Issue - State: closed - Opened by mmokrejs over 8 years ago - 1 comment

#27 - Spanning deletions aren't included in depth calculations

Issue - State: open - Opened by ernfrid almost 9 years ago
Labels: bug

#26 - VarScan fpfilter returning no results

Issue - State: open - Opened by ernfrid almost 9 years ago - 2 comments

#25 - A error report about bam-readcount

Issue - State: open - Opened by WinterLi1993 about 9 years ago - 3 comments

#24 - Does not report results for some 1-position regions

Issue - State: open - Opened by IgorFobia about 9 years ago - 5 comments
Labels: enhancement

#23 - pre-build dependency handling

Pull Request - State: closed - Opened by tabbott over 9 years ago - 6 comments

#22 - Parallel make fails

Issue - State: closed - Opened by sjackman over 9 years ago - 4 comments

#21 - `make install` ignores CMAKE_INSTALL_PREFIX

Issue - State: closed - Opened by sjackman over 9 years ago - 2 comments

#20 - Updated the bam-readcount command line 'usage' information

Pull Request - State: closed - Opened by morgantaschuk over 9 years ago - 2 comments

#19 - max depth still 8000 with -d set up

Issue - State: open - Opened by trptyrphe11 over 9 years ago - 4 comments
Labels: bug

#18 - Support for CRAM

Issue - State: open - Opened by smacarthur over 9 years ago - 8 comments
Labels: enhancement

#17 - use c++0x to fix segfault on Mac

Pull Request - State: closed - Opened by ernfrid almost 10 years ago - 1 comment

#16 - Quit spewing millions of warning messages by default

Issue - State: open - Opened by ernfrid almost 10 years ago - 1 comment
Labels: enhancement

#15 - bam-readcount does not install on centos 5

Issue - State: closed - Opened by dnjiao almost 10 years ago - 2 comments

#14 - Feature Request: Specify Flags to Include/Exclude

Issue - State: open - Opened by ernfrid almost 10 years ago - 3 comments
Labels: enhancement

#13 - Feature Request: Statistics per strand

Issue - State: open - Opened by smacarthur about 10 years ago - 3 comments
Labels: enhancement

#12 - segmentation faults on OSX 10.9.2 with Samtools 0.1.19-44428cd

Issue - State: closed - Opened by lordzappo over 10 years ago - 10 comments
Labels: bug

#11 - bugfix: make sure indel queue gets cleared

Pull Request - State: closed - Opened by tabbott over 10 years ago

#10 - fix gtest issues w/recent OS X compilers

Pull Request - State: closed - Opened by tabbott over 10 years ago

#9 - does not compile on OSX 10.9.2 with Samtools 0.1.19-44428cd

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

#5 - pileup_func: Bug fix when the Zm tag is missing

Pull Request - State: closed - Opened by sjackman over 11 years ago - 3 comments

#3 - Maximum depth defaults to 8000

Issue - State: closed - Opened by sjackman over 11 years ago - 20 comments

#2 - Many single-end mapping quality warnings

Issue - State: closed - Opened by sjackman over 11 years ago - 20 comments