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
#1971 - `FOLD_80_BASE_PENALTY` Metric from `TargetMetricsCollector` does not exclude 0 coverage regions.
Issue -
State: open - Opened by Patrick-Schlaeger-Broad 2 months ago
#1971 - `FOLD_80_BASE_PENALTY` Metric from `TargetMetricsCollector` does not exclude 0 coverage regions.
Issue -
State: open - Opened by Patrick-Schlaeger-Broad 2 months ago
#1970 - Can CollectWgsMetrics fall back to slow algorithm gracefully if the fast one fails with the default read length?
Issue -
State: open - Opened by gokalpcelik 3 months ago
- 7 comments
#1970 - Can CollectWgsMetrics fall back to slow algorithm gracefully if the fast one fails with the default read length?
Issue -
State: open - Opened by gokalpcelik 3 months ago
- 6 comments
#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
#1960 - Update AbstractAlignmentMerger.java Warning Message for Cross Species Contamination
Pull Request -
State: closed - Opened by gokalpcelik 5 months ago
#1960 - Update AbstractAlignmentMerger.java Warning Message for Cross Species Contamination
Pull Request -
State: closed - Opened by gokalpcelik 5 months ago
#1959 - `--USE_END_IN_UNPAIRED_READS` and `--USE_UNPAIRED_CLIPPED_END` options for `picard MarkDuplicates` have no effect
Issue -
State: open - Opened by ChrisHIV 6 months ago
- 9 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
#1955 - Allow fingerprinting of SAM files that only have a partial dictionary match to the haplotype map
Pull Request -
State: closed - Opened by yfarjoun 6 months ago
- 3 comments
#1955 - Allow fingerprinting of SAM files that only have a partial dictionary match to the haplotype map
Pull Request -
State: closed - Opened by yfarjoun 6 months ago
- 3 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
#1943 - genotypeConcordance irregular behavior in counting after applying filters
Issue -
State: closed - Opened by Dahn-YoungDong 7 months ago
- 3 comments
#1942 - MarkDuplicates strategy of flow based reads that looks only at the qualities close to the end of the read
Pull Request -
State: closed - Opened by ilyasoifer 8 months ago
#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
#1936 - MarkDuplicates: Instead of adding the read group of a read to the key, picard always adds "RG"
Issue -
State: closed - Opened by michaelgatzen 9 months ago
#1935 - Error: A JNI error has occurred, please check your installation and try again
Issue -
State: closed - Opened by Portulaca666 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
#1928 - Add flag to keep zero length intervals when converting bed -> interval_list
Pull Request -
State: closed - Opened by rickymagner 10 months ago
#1927 - Streaming from requester-pays buckets for CrosscheckFingerprints doesn't work in Terra
Issue -
State: open - Opened by rickymagner 10 months ago
- 2 comments
#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: open - Opened by RSchley 10 months ago
- 1 comment
#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
#1916 - warning: unable to load libgkl_compression.so from native/libgkl_compression.so (permission denied)
Issue -
State: closed - Opened by Ming-Yu615 11 months ago
#1915 - java.io.FileNotFoundException: /tmp/CSPI.tmp15948393444880722616/7573.tmp (Too many open files)
Issue -
State: closed - Opened by poojancf 11 months ago
- 1 comment
#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
#1907 - --TMP_DIR parameter is ignored and tmp dir defaults to /tmp for CollectInsertSizeMetrics (and possibly more picard tools))
Issue -
State: closed - Opened by gokalpcelik about 1 year ago
- 1 comment
Labels: bug
#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
#1896 - Guide to Installing OpenJDK Version 1.8.0_352 on Ubuntu for Picard Tool Compatibility
Issue -
State: closed - Opened by Sadiki-Noureddine over 1 year ago
- 1 comment
#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
#1891 - Fix #1081. Make --USE_SEQUENTIAL_FASTQS help message more user friendly
Pull Request -
State: closed - Opened by nrockweiler over 1 year ago
#1890 - BedToIntervalList reportedly does not handle stdin properly
Issue -
State: closed - Opened by droazen over 1 year ago
- 2 comments
Labels: stdin/stdout