Ecosyste.ms: Issues

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

GitHub / broadinstitute/picard issues and pull requests

#1977 - Fix documentation for AT_DROPOUT and GC_DROPOUT in PanelMetricsBase.java

Pull Request - State: closed - Opened by kockan about 1 month ago

#1976 - [issue-1959] MarkDuplicates flow options now start with FLOW_

Pull Request - State: open - Opened by dror27 about 1 month ago

#1976 - [issue-1959] MarkDuplicates flow options now start with FLOW_

Pull Request - State: open - Opened by dror27 about 1 month ago

#1975 - Refactor code around cloud support

Pull Request - State: open - Opened by takutosato about 2 months ago - 1 comment

#1974 - Add piped input tests for RevertSam, MergeBamAlignment

Pull Request - State: closed - Opened by takutosato about 2 months ago - 1 comment

#1973 - CollectHsMetrics AT_DROPOUT

Issue - State: closed - Opened by jcharlton67 about 2 months ago - 1 comment

#1973 - CollectHsMetrics AT_DROPOUT

Issue - State: open - Opened by jcharlton67 about 2 months ago

#1972 - Fold80 Bug Fix

Pull Request - State: open - Opened by Patrick-Schlaeger-Broad 2 months ago

#1972 - Fold80 Bug Fix

Pull Request - State: open - Opened by Patrick-Schlaeger-Broad 2 months ago

#1969 - Fix duplicate publishing issue

Pull Request - State: closed - Opened by lbergelson 3 months ago

#1968 - Update http-nio to 1.1.1

Pull Request - State: closed - Opened by droazen 3 months ago

#1967 - update htsjdk to 4.1.1

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

#1966 - Lost output/information during RenameSampleInVcf

Issue - State: closed - Opened by desmodus1984 4 months ago - 11 comments

#1965 - No more header requried for ribosomal interval files in CollectRnaSeqMetrics

Pull Request - State: closed - Opened by jourdren 4 months ago - 2 comments

#1964 - CollectWgsMetrics error, out of bound of the index?

Issue - State: closed - Opened by juanboja 4 months ago - 8 comments

#1963 - ValidateSamFile wrong NM tag computation

Issue - State: open - Opened by albertocasagrande 4 months ago - 3 comments

#1962 - Optical duplicates

Issue - State: closed - Opened by Nitin123-4 5 months ago - 4 comments

#1961 - MarkDuplicates SAM validation error

Issue - State: closed - Opened by vivekbibs 5 months ago - 6 comments

#1958 - Running picard in parallel issue

Issue - State: closed - Opened by Davood-Norouzi 6 months ago - 3 comments

#1957 - UnMarkDuplicate

Issue - State: closed - Opened by Davood-Norouzi 6 months ago - 1 comment

#1956 - -fixes a bug in the liftover logic whereby when the alleles couldn't …

Pull Request - State: closed - Opened by yfarjoun 6 months ago - 5 comments

#1956 - -fixes a bug in the liftover logic whereby when the alleles couldn't …

Pull Request - State: open - Opened by yfarjoun 6 months ago - 5 comments

#1954 - about MarkDuplicates

Issue - State: open - Opened by cnxiaobo94 6 months ago

#1954 - about MarkDuplicates

Issue - State: closed - Opened by cnxiaobo94 6 months ago - 1 comment

#1953 - Issue Running Picard MarkDuplicates: File Compression Error with Snappy

Issue - State: closed - Opened by VPatel294 6 months ago - 1 comment

#1952 - TAGGING_POLICY=OpticalOnly tags everything

Issue - State: open - Opened by Davood-Norouzi 6 months ago - 4 comments

#1952 - TAGGING_POLICY=OpticalOnly tags everything

Issue - State: closed - Opened by Davood-Norouzi 6 months ago - 4 comments

#1951 - Edge case in LiftoverVcf causes cryptic string exception

Issue - State: open - Opened by rickymagner 6 months ago - 4 comments

#1951 - Edge case in LiftoverVcf causes cryptic string exception

Issue - State: closed - Opened by rickymagner 6 months ago - 8 comments

#1950 - How to control the number of threads

Issue - State: closed - Opened by yitengfei120011 6 months ago - 1 comment

#1949 - Cloudify RevertSam

Pull Request - State: closed - Opened by takutosato 7 months ago - 5 comments

#1948 - Getting Segfault when running ReorderSam via GATK

Issue - State: closed - Opened by rickymagner 7 months ago - 1 comment

#1947 - java environment not detected when using option OUTPUT in BuilBamIndex

Issue - State: closed - Opened by r-poloni 7 months ago - 1 comment

#1946 - Picard Build Failure

Issue - State: closed - Opened by n-belle 7 months ago - 6 comments

#1945 - Fix for order flipping in SortingCollection used for MarkDuplicates

Pull Request - State: closed - Opened by wook-choi 7 months ago - 1 comment

#1944 - MarkDuplicates with single end data does not write the full report

Issue - State: open - Opened by mattsoup 7 months ago - 3 comments

#1941 - java.lang.NegativeArraySizeException

Issue - State: closed - Opened by pk-zhu 8 months ago - 2 comments

#1940 - DRAFT - ignore me.

Pull Request - State: closed - Opened by cmnbroad 9 months ago

#1939 - Update setup_gcloud github action

Pull Request - State: closed - Opened by lbergelson 9 months ago

#1938 - Add new argument to allow setting the google requester pays project

Pull Request - State: open - Opened by lbergelson 9 months ago - 2 comments

#1937 - MarkDuplicates: Add read group ID instead of string "RG"

Pull Request - State: closed - Opened by michaelgatzen 9 months ago - 1 comment

#1934 - Convert to use the java-library plugin

Pull Request - State: closed - Opened by lbergelson 9 months ago

#1933 - StringIndexOutOfBoundsException at LiftoverVcf

Issue - State: closed - Opened by C37H41N2O6 9 months ago - 3 comments

#1932 - CollectQualityYieldMetricsFlowSpace tool

Pull Request - State: closed - Opened by dror27 9 months ago - 14 comments

#1931 - Test updating to java 21

Pull Request - State: open - Opened by lbergelson 10 months ago

#1930 - Update Gradle to 8.5

Pull Request - State: closed - Opened by lbergelson 10 months ago

#1929 - Adding http-nio as a dependency

Pull Request - State: closed - Opened by lbergelson 10 months ago - 1 comment

#1926 - Problem with Picard tool for Collecting RNASeqMetrics

Issue - State: closed - Opened by annepureddy 10 months ago - 4 comments

#1925 - Cloud support for BuildBamIndex outputs.

Pull Request - State: open - Opened by cmnbroad 10 months ago - 1 comment

#1924 - CollectHsMetrics returns negative percentages on PacBio data

Issue - State: closed - Opened by valeandri 10 months ago - 5 comments

#1923 - picard MarkDuplicates error: Value was put into PairInfoMap more than once

Issue - State: closed - Opened by RSchley 10 months ago - 2 comments

#1922 - MBA documentation

Pull Request - State: closed - Opened by kachulis 11 months ago

#1921 - Update Dockerfile and build_push_docker.sh

Pull Request - State: closed - Opened by lbergelson 11 months ago

#1920 - Updated the SamToFastq documentation

Pull Request - State: closed - Opened by kockan 11 months ago - 1 comment

#1919 - Switch transitive dependencies from runtime to compile

Pull Request - State: closed - Opened by kshakir 11 months ago - 3 comments

#1918 - Reject piped input (/dev/stdin) for BedToIntervalList

Pull Request - State: closed - Opened by kockan 11 months ago - 1 comment

#1917 - Update htsjdk to 4.0.2

Pull Request - State: closed - Opened by lbergelson 11 months ago

#1914 - BedToIntervalList doesn't handle empty bed region edge cases properly

Issue - State: closed - Opened by rickymagner about 1 year ago - 8 comments

#1913 - Fix CollectHSMetrics - Don't use Coverage Cap on fold score

Pull Request - State: closed - Opened by JoeVieira about 1 year ago - 19 comments

#1912 - INVALID_ALIGNMENT_START

Issue - State: closed - Opened by miderxi about 1 year ago - 4 comments

#1911 - unable to run picard

Issue - State: closed - Opened by shanmugavadivelps about 1 year ago - 2 comments

#1910 - FastqToSam stdin fix for #915

Pull Request - State: closed - Opened by delocalizer about 1 year ago - 1 comment

#1909 - Check for non-symbolic alt alleles before left aligning in liftover

Pull Request - State: closed - Opened by kachulis about 1 year ago

#1908 - Trying out an easy fix for setting the custom tmp folder.

Pull Request - State: closed - Opened by kockan about 1 year ago - 4 comments

#1906 - Question marks in output of Picard tools

Issue - State: closed - Opened by Yu-jinKim about 1 year ago - 5 comments

#1905 - Installation problem of v3.1.0

Issue - State: closed - Opened by FionaMoon about 1 year ago - 4 comments

#1904 - Fix gradle 8 publishing issue

Pull Request - State: closed - Opened by kshakir about 1 year ago - 1 comment

#1903 - Update google-cloud-nio to support underscores in bucket names

Pull Request - State: closed - Opened by kshakir about 1 year ago - 3 comments

#1902 - typo correction "Didn't recognized" -> "Didn't recognize"

Pull Request - State: closed - Opened by tomkinsc about 1 year ago

#1901 - Update all our dependencies to the latest version

Pull Request - State: closed - Opened by lbergelson about 1 year ago - 1 comment

#1900 - make cloud jar mandatory

Pull Request - State: closed - Opened by lbergelson about 1 year ago

#1899 - Creating

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

#1898 - Picard Cloud

Issue - State: closed - Opened by lappazos about 1 year ago - 2 comments

#1897 - Conda installer

Issue - State: open - Opened by lappazos about 1 year ago - 8 comments

#1895 - Fix the dependency issue causing dsp-appsec-trivy workflow to fail.

Pull Request - State: closed - Opened by kockan over 1 year ago

#1894 - picard markduplicate issue

Issue - State: closed - Opened by Subhajeet1997 over 1 year ago - 2 comments

#1893 - Inconsistencies in Picard MarkDuplicates Histogram Data Output

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

#1892 - Changed CrosscheckFingerprints hashing to linked hashing

Pull Request - State: closed - Opened by tmelman over 1 year ago - 4 comments

#1890 - BedToIntervalList reportedly does not handle stdin properly

Issue - State: closed - Opened by droazen over 1 year ago - 2 comments
Labels: stdin/stdout