Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / enasequence/cramtools issues and pull requests
#76 - Tutorial for CRAM tools
Issue -
State: open - Opened by gadepallivs almost 7 years ago
#75 - Cramtools merge error
Issue -
State: open - Opened by HovhannesSahakyan almost 7 years ago
- 5 comments
#74 - Error with cramtools 3.0 - Error downloading ref and exception handle
Issue -
State: open - Opened by Prathyusha-konda almost 7 years ago
- 1 comment
#73 - Cannot convert CRAM back to BAM
Issue -
State: open - Opened by loganjeverett about 7 years ago
- 3 comments
#72 - Exception in thread "main" java.lang.reflect.InvocationTargetException
Issue -
State: open - Opened by tseemann about 7 years ago
#71 - cramtools index error
Issue -
State: open - Opened by pwaltman over 7 years ago
#70 - cram to bam conversion error
Issue -
State: open - Opened by blueagave over 7 years ago
- 1 comment
#69 - cram tools internet connection requirement - undocumented behaviour
Issue -
State: open - Opened by MikeDMorgan over 7 years ago
#68 - Build fail due to non-ascii characters
Issue -
State: open - Opened by jkbonfield over 7 years ago
#67 - Junit test submit shivika
Pull Request -
State: open - Opened by shivikas almost 8 years ago
#66 - Technical test vikhorev
Pull Request -
State: open - Opened by avikhorev almost 8 years ago
#65 - Problem converting CRAM back to BAM
Issue -
State: open - Opened by kalexiou almost 8 years ago
- 25 comments
#64 - failed to add reference
Issue -
State: open - Opened by kygpp almost 8 years ago
#63 - build fail
Issue -
State: open - Opened by SooLee almost 8 years ago
#62 - Misleading @PG-CL header generated
Issue -
State: open - Opened by jmarshall almost 8 years ago
#61 - cram 2 fastq: header format
Issue -
State: open - Opened by ingkebil almost 8 years ago
#60 - CRAM to BAM fail on large file
Issue -
State: open - Opened by Arkarachai about 8 years ago
- 11 comments
#59 - cramtools-3.0/src/main/java/htsjdk/samtools/cram/lossy/Binning.java:61: error: unmappable character for encoding ASCII
Issue -
State: open - Opened by mmokrejs about 8 years ago
- 1 comment
#58 - Change default in build.xml to "compile"
Issue -
State: open - Opened by mmokrejs about 8 years ago
#57 - lose quality score from BAM -> CRAM -> BAM conversion
Issue -
State: open - Opened by Arkarachai over 8 years ago
- 3 comments
#56 - Cram2Fastq Conversion flip the reads for one of the pairs in paired-end sequencing?
Issue -
State: open - Opened by minisciencegirl over 8 years ago
- 8 comments
#55 - Java Error
Issue -
State: closed - Opened by tinuthomas over 8 years ago
- 1 comment
#54 - improved readability of README file
Pull Request -
State: closed - Opened by zyxue over 8 years ago
- 1 comment
#53 - Count records in *.cram fails with FileNotFoundException
Issue -
State: open - Opened by iromeo over 8 years ago
- 10 comments
#52 - BAM to CRAM conversion: Error:New position is beyond the reference: 1
Issue -
State: open - Opened by ghost over 8 years ago
- 3 comments
#51 - Index piped cram file
Issue -
State: open - Opened by GWarsow over 8 years ago
- 5 comments
#50 - fastq: add option to split by read group
Issue -
State: open - Opened by vadimzalunin over 8 years ago
- 1 comment
#49 - fastq for paired-end sequencing
Issue -
State: open - Opened by vcaropr1 over 8 years ago
- 2 comments
#48 - Lossy compression: cramtools 2.1 outperforms other implementations
Issue -
State: open - Opened by jacrayner almost 9 years ago
- 12 comments
#47 - Cram2Bam aborts based on file extension of fasta reference
Issue -
State: closed - Opened by yhoogstrate almost 9 years ago
#46 - Bam2Cram is slow
Issue -
State: open - Opened by superbobry almost 9 years ago
- 1 comment
#45 - Unindexed FASTA might lead to NPE
Issue -
State: open - Opened by superbobry almost 9 years ago
- 1 comment
#44 - Runtime exception while converting the bam to fastq
Issue -
State: open - Opened by sc8998 almost 9 years ago
#43 - best approach for lossless compression
Issue -
State: open - Opened by RichardCorbett about 9 years ago
- 4 comments
#42 - 3.0 noclassdef errors
Issue -
State: open - Opened by RichardCorbett about 9 years ago
- 8 comments
#41 - Content hash mismatch for tag BD
Issue -
State: open - Opened by GWarsow about 9 years ago
#40 - Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
Issue -
State: open - Opened by btiernay about 9 years ago
- 18 comments
#39 - Htsjdk 1.136
Pull Request -
State: closed - Opened by vadimzalunin about 9 years ago
#38 - NPE in Cram2Bam for refid -2
Issue -
State: closed - Opened by vadimzalunin about 9 years ago
- 1 comment
Labels: bug
#37 - Supplementary reads need to be supported
Issue -
State: open - Opened by jkbonfield over 9 years ago
- 6 comments
#36 - RG lines are created where they should not exist
Issue -
State: open - Opened by jkbonfield over 9 years ago
- 1 comment
#35 - CIGAR alignment length changed for sequence "*"
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 4 comments
#34 - CIGAR "N" produces incorrect sequence when decoding.
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 1 comment
#33 - Regression: some v2.1 files cannot be decoded by 3.0
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 1 comment
#32 - Typo in code
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 1 comment
#31 - Unsorted data crash in gamma codec
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 2 comments
#30 - MD5 on reference sequences that are too short
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 2 comments
#29 - >= 129 auxiliary tags
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 10 comments
#28 - Support for multiple reference containers.
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 5 comments
#27 - Content hash mismatch for tag SD
Issue -
State: open - Opened by jkbonfield over 9 years ago
- 7 comments
#26 - Sequence * with cigar strings
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 2 comments
#25 - Error decoding c1#pad1.tmp.cram
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 4 comments
#24 - CRAM with data out of bounds causes a Java stack trace.
Issue -
State: open - Opened by jkbonfield over 9 years ago
- 8 comments
#23 - Unmapped read decoding failure
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 1 comment
#22 - Cramtools 3.0 decoding error
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 1 comment
#21 - CRAM 3.0 position change for unmapped reads
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 1 comment
#20 - Cramtools-3.0.jar error
Issue -
State: closed - Opened by jkbonfield over 9 years ago
- 6 comments
#19 - More build file updates and some new junit tests.
Pull Request -
State: closed - Opened by fduckart over 9 years ago
- 2 comments
#18 - Update build so that the test target will run all the junit tests.
Pull Request -
State: closed - Opened by fduckart over 9 years ago
- 1 comment
#17 - Exception running ValidateCramFile
Issue -
State: open - Opened by hreuver over 9 years ago
- 13 comments
#16 - Strange exception behaviour
Issue -
State: closed - Opened by hreuver over 9 years ago
- 4 comments
#15 - sam roundtrip does not respect N in cigar
Issue -
State: open - Opened by vadimzalunin almost 10 years ago
#14 - NullPointerException at Bam2Cram.java:283
Issue -
State: closed - Opened by JimKent over 10 years ago
- 5 comments
#13 - cramtools package name is illigetimate and confusing
Issue -
State: open - Opened by diekhans over 10 years ago
- 2 comments
#12 - add proper support for multi-fragment reads
Issue -
State: open - Opened by vadimzalunin over 10 years ago
#11 - X vs B read features
Issue -
State: open - Opened by vadimzalunin over 10 years ago
#10 - NoClassDefFoundError in 2.1
Issue -
State: closed - Opened by boboppie over 10 years ago
- 5 comments
#9 - Problem with fastq command?
Issue -
State: closed - Opened by flashton2003 over 10 years ago
- 2 comments
#8 - Update README
Pull Request -
State: closed - Opened by flashton2003 over 10 years ago
#7 - print out variations
Issue -
State: open - Opened by vadimzalunin over 10 years ago
#6 - Support for XZ compression
Issue -
State: open - Opened by reedacartwright almost 11 years ago
#5 - EOF marker similar to BAM
Issue -
State: open - Opened by vadimzalunin almost 11 years ago
#4 - getref option typo: "warp" vs "wrap"
Issue -
State: closed - Opened by tseemann almost 11 years ago
- 1 comment
#3 - Handling of sequences beyond reference extents.
Issue -
State: open - Opened by jkbonfield about 11 years ago
Labels: bug
#2 - MD5sum checking
Issue -
State: closed - Opened by jkbonfield about 11 years ago
- 1 comment
Labels: bug
#1 - Lossless compression ?
Issue -
State: closed - Opened by brunoli about 11 years ago
- 1 comment
Labels: wontfix