GregoryFaust/samblaster issues and pull requests

#58 - Can't find first and/or second of pair in sam block of length

Issue - State: open - Opened by CaroleBelliardo over 1 year ago - 1 comment

#57 - Aligning in Biscuit with samblaster and samtools

Issue - State: open - Opened by KChadwick78 over 1 year ago - 1 comment

#56 - how do samblaster define a split read?

Issue - State: closed - Opened by WZo0o about 2 years ago - 2 comments

#55 - Duplicates were removed but log says 0 dups removed

Issue - State: open - Opened by sehawk about 2 years ago - 1 comment

#54 - Pipe output to samblaster from bwa-mem2

Issue - State: closed - Opened by Talo07 over 3 years ago - 1 comment

#53 - add support for read group and PCR free optitical duplicate only filtering

Pull Request - State: open - Opened by carsonhh over 3 years ago

#52 - Please adapt the metrics

Issue - State: open - Opened by ToVste over 3 years ago

#51 - Option to remove split and disc alignments?

Issue - State: open - Opened by biobenkj almost 4 years ago - 1 comment

#50 - unmated reads

Issue - State: closed - Opened by jvanalstine about 4 years ago - 1 comment

#49 - Alpine-based docker build fails

Issue - State: open - Opened by felixfrenkel over 4 years ago - 1 comment

#48 - walltime is twice cpu seconds

Issue - State: open - Opened by jsmedmar over 4 years ago - 3 comments

#47 - can samblaster tackle reads with UMI?

Issue - State: open - Opened by windtalker6 over 4 years ago - 1 comment

#46 - Very different result between samtools and samblaster

Issue - State: closed - Opened by biozzq over 4 years ago - 3 comments

#45 - Can't find first and/or second of pair error

Issue - State: open - Opened by dheerajbobbili1988 almost 5 years ago - 1 comment

#44 - Avoid warning about missing space around literal

Pull Request - State: closed - Opened by marcelm almost 5 years ago - 1 comment

#43 - Segmentation fault on getting split reads from long read file?

Issue - State: closed - Opened by cmdcolin over 5 years ago - 7 comments

#42 - Getting splitters BAM from long reads data?

Issue - State: closed - Opened by cmdcolin over 5 years ago - 7 comments

#41 - Duplicate `MC` tags in samblaster output

Issue - State: closed - Opened by DonFreed over 5 years ago - 6 comments

#40 - remove duplicate for single-end read

Issue - State: closed - Opened by timedreamer over 5 years ago - 4 comments

#39 - Can not run MarkDup for very large bam file

Issue - State: closed - Opened by liujiayi771 almost 6 years ago - 1 comment

#38 - Support for DT tag to distinguish PCR and optical duplicates

Issue - State: open - Opened by seboyden over 6 years ago - 6 comments

#37 - Can't find first and/or second of pair in sam block of length 1 for id:...

Issue - State: closed - Opened by bibbers93 almost 7 years ago - 3 comments

#36 - threading

Issue - State: closed - Opened by ttriche almost 7 years ago - 5 comments

#35 - Filter out soft/hard clipped reads in a pipe SAM -> SAM ?

Issue - State: open - Opened by tseemann almost 7 years ago - 5 comments

#34 - split reads detection parameters

Issue - State: closed - Opened by alantsangmb about 7 years ago - 1 comment

#33 - spitters : I don't get understand the code :-)

Issue - State: closed - Opened by lindenb about 7 years ago - 1 comment

#32 - Is samblaster readgroup aware?

Issue - State: closed - Opened by crazyhottommy about 7 years ago - 4 comments

#31 - discordant read pairs and split reads

Issue - State: closed - Opened by WortJohn over 7 years ago - 1 comment

#30 - Read pair detection failure from biscuit-aligned reads

Issue - State: closed - Opened by tantrev over 7 years ago - 6 comments

#29 - Fix broken headings in Markdown files

Pull Request - State: closed - Opened by bryant1410 almost 8 years ago

#28 - output file option segmentation fault

Issue - State: closed - Opened by mken418 almost 8 years ago - 1 comment

#27 - Question about "A read-id grouped SAM file"

Issue - State: closed - Opened by jiadong324 over 8 years ago - 2 comments

#26 - segfault during hashTableInsert

Issue - State: closed - Opened by chapmanb over 8 years ago - 3 comments

#25 - Plans to use htslib ?

Issue - State: closed - Opened by tseemann over 8 years ago - 2 comments

#24 - Don't add MC and MQ tags to a read if its mate is unmapped

Pull Request - State: closed - Opened by ernfrid over 8 years ago - 1 comment

#23 - Handle chrM discordants differently

Issue - State: open - Opened by jdidion over 8 years ago

#22 - More info for missing pair

Issue - State: closed - Opened by zeeev over 8 years ago - 4 comments

#21 - non-human genomes with many contigs

Issue - State: closed - Opened by carsonhh almost 9 years ago - 5 comments

#20 - Support for UMIs

Issue - State: open - Opened by mjafin almost 9 years ago - 6 comments

#19 - Too many sequences in header of input sam file

Issue - State: closed - Opened by vladimirkovacevic almost 9 years ago - 7 comments

#18 - after extracting disc and split reads, does the final bam still contain them?

Issue - State: closed - Opened by crazyhottommy over 9 years ago - 1 comment

#17 - added -m/-metricsFile flag to output duplication metrics

Pull Request - State: closed - Opened by dakl over 9 years ago - 6 comments

#16 - Write duplication metrics to file

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

#15 - workaround for bam files with some singleton reads

Issue - State: closed - Opened by elzbth almost 10 years ago - 6 comments

#14 - Makefile error OS X

Issue - State: closed - Opened by LeahRoberts almost 10 years ago - 2 comments

#13 - Avoid buffer length issues when marking long SAM lines

Pull Request - State: closed - Opened by chapmanb almost 10 years ago - 2 comments

#12 - Mate tags

Issue - State: closed - Opened by cc2qe almost 10 years ago - 1 comment

#11 - Support multiple clipping operations at the beginning of a read

Issue - State: closed - Opened by ernfrid almost 10 years ago - 3 comments

#10 - Add support for N opcode

Issue - State: closed - Opened by holtgrewe almost 10 years ago - 5 comments

#9 - Support for BED files?

Issue - State: closed - Opened by samhunter almost 10 years ago - 2 comments

#8 - Fixes for MacOS

Pull Request - State: closed - Opened by saketkc about 10 years ago - 1 comment

#7 - Support for OS X.

Pull Request - State: closed - Opened by aakrosh over 10 years ago

#6 - Support sequence match (=) and mismatch (X) in CIGAR strings.

Pull Request - State: closed - Opened by chapmanb over 10 years ago - 1 comment

GitHub / GregoryFaust/samblaster issues and pull requests