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

#1889 - DbSnpBitSetUtil should verify that the VCF dict should match the inpu…

Pull Request - State: closed - Opened by nh13 over 1 year ago - 3 comments

#1888 - PICARD termination ,

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

#1887 - Fix deprecated uses of newInstance()

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

#1886 - Add .DS_STORE and .java-version to .gitignore

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

#1885 - Enable IntelInflater

Pull Request - State: closed - Opened by lbergelson over 1 year ago - 2 comments

#1883 - Picard build failed

Issue - State: closed - Opened by jiachenli1218 over 1 year ago - 1 comment

#1881 - Samtofastq does not retain all the information

Issue - State: closed - Opened by ajeyab22 over 1 year ago - 5 comments

#1880 - DRAFT: VCFHeader refactoring

Pull Request - State: open - Opened by cmnbroad over 1 year ago

#1879 - Mark Duplicates - Not Enough Fields Exception

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

#1874 - BUILD FAILED error

Issue - State: closed - Opened by HK0911 over 1 year ago - 1 comment

#1873 - CollectSamErrorMetrics overlap total bases

Issue - State: closed - Opened by kachulis over 1 year ago - 1 comment

#1872 - CONVERT BAM TO U-BAM Error

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

#1871 - Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector

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

#1870 - More informative error messages when dictionaries don't match

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

#1869 - Sequence dictionaries are not the same size

Issue - State: closed - Opened by pd3 over 1 year ago - 5 comments

#1868 - Refactoring

Pull Request - State: closed - Opened by LadDeep over 1 year ago - 8 comments

#1867 - Question about Depth

Issue - State: closed - Opened by Nour-EddineS over 1 year ago - 1 comment

#1866 - Sum of Which columns in MarkDulicates metrices gives us total reads?

Issue - State: closed - Opened by Rohit-Satyam over 1 year ago - 1 comment

#1865 - GENOTYPING_ERROR_RATE doesn't do anything in CrosscheckFingerprints

Issue - State: closed - Opened by kachulis over 1 year ago - 3 comments

#1864 - SamToFastq

Issue - State: closed - Opened by ruinw over 1 year ago - 5 comments

#1863 - Picard new release

Issue - State: closed - Opened by lappazos over 1 year ago - 6 comments

#1861 - OutOfMemoryError

Issue - State: closed - Opened by TKsh6 over 1 year ago - 2 comments

#1860 - Lb add cloud tests

Pull Request - State: closed - Opened by lbergelson over 1 year ago - 2 comments

#1859 - Allow empty input files for CollectAlignmentSummaryMetrics and FastqToSam

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

#1858 - Remove obsolete references to Google Genomics API

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

#1857 - Delete the now redundant ClassFinder

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

#1855 - Switch to Java 17.

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

#1854 - Order of rows in crosscheck metrics files are non-deterministic

Issue - State: open - Opened by kachulis over 1 year ago - 4 comments

#1853 - Adding a gh actions test

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

#1852 - Support cloud input/output for IntervalListTools

Pull Request - State: closed - Opened by takutosato over 1 year ago - 7 comments

#1851 - SamToFastq writes to /dev/stdout Exception

Issue - State: closed - Opened by yingwei13mei over 1 year ago - 1 comment

#1850 - Check "CHART_OUTPUT != null" before generating a pdf

Pull Request - State: open - Opened by yatzek over 1 year ago - 3 comments

#1849 - Remove unused method Fingerprint.filterSuspectSites()

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

#1848 - Possible MarkDuplicates bug: no optical duplicates found

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

#1847 - CollectAlignmentSummaryMetrics throws exception upon an empty BAM file (header only)

Issue - State: closed - Opened by nh13 almost 2 years ago - 2 comments
Labels: bug

#1845 - Thresholds for AT_DROPOUT and GC_DROPOUT

Issue - State: closed - Opened by Newbee-glitch almost 2 years ago - 1 comment

#1844 - chore: bump htsjdk to 3.0.3

Pull Request - State: closed - Opened by clintval almost 2 years ago - 4 comments

#1843 - Fix Duplicate Set Index for queryname sorted input to MarkDuplicates

Pull Request - State: closed - Opened by kachulis almost 2 years ago - 1 comment

#1842 - Fix typo in a filter name output by LiftoverVcf

Pull Request - State: closed - Opened by lbergelson almost 2 years ago

#1840 - testBamToBfq output changed when switching from OpenJDK11 to OpenJDK17

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

#1839 - Improvements to CompareMetrics

Pull Request - State: closed - Opened by kachulis almost 2 years ago

#1838 - Fix bai location when output not specified for BuildBamIndex

Pull Request - State: closed - Opened by kachulis almost 2 years ago - 3 comments

#1837 - Updated the issue template to link to our support forum

Pull Request - State: closed - Opened by droazen almost 2 years ago - 1 comment

#1836 - CrosscheckFingerprints : Sequences at index 0 don't match:

Issue - State: closed - Opened by MjelleLab almost 2 years ago - 1 comment

#1835 - CollectSamErrorMetrics error

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

#1834 - Update request to SamToFastq documentation

Issue - State: closed - Opened by GATKSupportTeam almost 2 years ago - 3 comments
Labels: docs

#1833 - Upgrade to Java 17.

Pull Request - State: closed - Opened by cmnbroad almost 2 years ago

#1832 - FilterSamReads not able to solve soft links for reference file

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

#1831 - Update htsjdk to 3.0.1

Pull Request - State: closed - Opened by lbergelson about 2 years ago - 2 comments

#1830 - Cannot find Output files after applying Markduplicates with picard tools

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

#1829 - Fix temporary directory hijacking or temporary directory information disclosure

Pull Request - State: closed - Opened by lbergelson about 2 years ago - 1 comment

#1828 - picard MarkDuplicates takes more than a day

Issue - State: closed - Opened by xl5525 about 2 years ago - 1 comment

#1827 - BuildBamIndex creates index file in the current directory

Issue - State: open - Opened by regnveig about 2 years ago - 9 comments

#1826 - This PR skips avoids merging fingerprints when there's only one finge…

Pull Request - State: closed - Opened by yfarjoun about 2 years ago - 2 comments

#1825 - Enables setting the google-project that will be charged for requests …

Pull Request - State: open - Opened by yfarjoun about 2 years ago - 2 comments

#1824 - UmiAwareMarkDuplicatesWithMateCigar (no duplex). How to use it correctly?

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

#1823 - Allow explicit index file paths for inputs to CrosscheckFingerprints

Pull Request - State: closed - Opened by rickymagner about 2 years ago - 5 comments

#1822 - mark duplicates according to the tag of Optional Fields in BAM file

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

#1821 - [SECURITY] Fix Temporary Directory Hijacking or Information Disclosure Vulnerability

Pull Request - State: closed - Opened by JLLeitschuh about 2 years ago - 1 comment

#1819 - Cannot build Extended Illumina Manifest

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

#1817 - No output generated for MarkDuplicatesWithMateCigar Picard tool

Issue - State: closed - Opened by Pravithaks over 2 years ago - 1 comment

#1816 - Problem with picard MarkDuplicates --version

Issue - State: closed - Opened by SenseeraMachine over 2 years ago - 1 comment

#1814 - MD5SUM from picard and samtools do not match

Issue - State: closed - Opened by fgvieira over 2 years ago - 8 comments
Labels: bug

#1813 - Picard modifications to support flow based sequencing

Pull Request - State: closed - Opened by ilyasoifer over 2 years ago - 6 comments

#1812 - Upgrade to htsjdk 3.0.0.

Pull Request - State: closed - Opened by cmnbroad over 2 years ago - 4 comments

#1811 - Fix FastqToSam regression.

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

#1810 - FastqToSam now breaks with gzipped FASTQ input

Issue - State: closed - Opened by mjhipp over 2 years ago - 1 comment

#1808 - CollectMultipleMetrics Skip making charts if R is not installed

Issue - State: open - Opened by nh13 over 2 years ago - 1 comment
Labels: R-Dependency

#1807 - Question about HsMetrics PCT_SELECTED_BASES

Issue - State: closed - Opened by kkamii over 2 years ago - 1 comment

#1806 - markDuplicates : Not removing all duplicates

Issue - State: closed - Opened by PriyaLakr over 2 years ago - 1 comment

#1805 - Filter HOM_REF records without GQ information

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

#1804 - Enable use of cloud reference files

Pull Request - State: closed - Opened by cmnbroad over 2 years ago - 17 comments

#1802 - Account for overlapping reads in Theoretical Sensitivity model

Pull Request - State: open - Opened by fleharty over 2 years ago - 2 comments

#1800 - MarkDuplicate memory issue

Issue - State: closed - Opened by guptapa over 2 years ago - 1 comment

#1799 - How to keep "duplicates" from different cells in single-cell sequencing data

Issue - State: closed - Opened by Yydtqqqg over 2 years ago - 1 comment

#1797 - Snappy Error on M1 mac when running SortSam

Issue - State: closed - Opened by RomeroMatt over 2 years ago - 4 comments

#1793 - Don't fail if R is not installed

Issue - State: open - Opened by paidi over 2 years ago - 1 comment
Labels: R-Dependency

#1788 - Add support for reading SAM/BAM files with contigs larger than max int

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

#1785 - Update command line parser argument style detection, add tests.

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

#1784 - mixed command line argument syntax throws too unspecific error message

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

#1779 - Make truncating the histogram optional in CollectInsertSizeMetrics

Pull Request - State: open - Opened by takutosato over 2 years ago - 4 comments

#1776 - Picard SortVcf has issues reading from `/dev/stdin` and writing to `/dev/stdout`

Issue - State: open - Opened by clintval over 2 years ago
Labels: stdin/stdout

#1773 - Memory footprint on MarkDuplicates?

Issue - State: closed - Opened by bbimber over 2 years ago - 4 comments

#1761 - xxx did not start with a parsable number

Issue - State: closed - Opened by jingydz almost 3 years ago - 4 comments

#1753 - Expose new CLI option in CheckFingerprint

Pull Request - State: closed - Opened by SHuang-Broad almost 3 years ago - 5 comments
Labels: Waiting For Revisions

#1737 - MarkDuplicates error could not create Java Virtual Machine

Issue - State: closed - Opened by us1399 almost 3 years ago - 1 comment