Ecosyste.ms: Issues

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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

#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

#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

#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

#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

#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