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
#1884 - Add tests to verify sequence dictionary MD5s respect dos line endings.
Pull Request -
State: closed - Opened by cmnbroad over 1 year ago
#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
#1878 - Mark GENOTYPING_ERROR_RATE as a DeprecatedFeature and remove code ref…
Pull Request -
State: closed - Opened by cmnbroad over 1 year ago
#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
#1862 - CollectAlignmentSummaryMetrics fails on some small inputs due to unsafe Histogram methods
Issue -
State: closed - Opened by rickymagner over 1 year ago
- 1 comment
#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
#1856 - Remove commons.lang dependency because it is redundant with commons lang3
Pull Request -
State: closed - Opened by lbergelson over 1 year ago
#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
#1846 - Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file
Issue -
State: closed - Opened by beaufor almost 2 years ago
- 3 comments
#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
#1841 - Typo in "IndelStraddlesMultipleIntevals". Should be "Intervals" instead of "Intevals"
Issue -
State: closed - Opened by bw2 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
#1820 - [SECURITY] Fix Temporary Directory Hijacking or Information Disclosure Vulnerability
Pull Request -
State: closed - Opened by JLLeitschuh about 2 years ago
#1819 - Cannot build Extended Illumina Manifest
Issue -
State: closed - Opened by yilevine about 2 years ago
- 1 comment
#1818 - Exception in thread "main" java.lang.IllegalStateException: Shutdown in progress
Issue -
State: closed - Opened by CherryX727 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
#1815 - Documentation request: Better examples of the inputs to ExtractIlluminaBarcodes, IlliminaBasecallsToFastq, and IlluminaBasecallsToSam
Issue -
State: open - Opened by bkohrn over 2 years ago
#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
#1809 - LiftoverVCF: "chain line has wrong number of fields in chain file" when 3 or more newlines are found after a chain entry block.osomal renaming
Issue -
State: closed - Opened by ghuls 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
#1803 - Bug report: A fatal error has been detected by the Java Runtime Environment
Issue -
State: open - Opened by Programjackanapes over 2 years ago
- 3 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
#1767 - HsMetrics "coverage cap" parameter affects more than theoretical sensitivity calculations
Issue -
State: closed - Opened by eboyden almost 3 years ago
- 6 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
#1741 - MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true does not add DS and DI tags in the output BAM file
Issue -
State: open - Opened by GATKSupportTeam almost 3 years ago
- 3 comments
#1737 - MarkDuplicates error could not create Java Virtual Machine
Issue -
State: closed - Opened by us1399 almost 3 years ago
- 1 comment
#1732 - CollectvariantCallingMetrics java.lang.NullPointerException for contigs not in the reference
Issue -
State: open - Opened by GATKSupportTeam almost 3 years ago
- 4 comments