amplab snap issues - Githubissues

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

https://www.microsoft.com/en-us/research/project/snap/

Apache License 2.0

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issues

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-F option yielding incongruous output

#119 cxr5298 opened 5 years ago
0
Add missing return statement

#118 liubovch closed 5 years ago
1
sort option -so expected functionality

#117 ramcn closed 3 years ago
1
snap speedup above 32 threads

#116 ramcn closed 4 years ago
2
Error - No overlapping contigs found during variant calling pre processing

#115 ramcn closed 6 years ago
5
snap showing high io utilization

#114 ramcn closed 6 years ago
2
Snap aligner FASTQ record larger than buffer

#113 klaas-men closed 4 years ago
3
Test failure on ppc64 and sparc64

#112 tillea opened 6 years ago
0
Does not build on 32 bit architectures

#111 tillea closed 4 years ago
2
Test suite failure on ppc64 and sparc64 architectures

#110 tillea opened 6 years ago
0
`soft_exit_no_print(1)` returns 1 instead of 0 when calling help

#109 mmterpstra closed 4 years ago
1
I got an error

#108 wangzhenkeep closed 4 years ago
1
GRCh38 HLA contig names get turned into invalid @SQ lines

#107 fnothaft closed 7 years ago
2
Cleaned up methylation

#106 akmorrow13 closed 7 years ago
2
Added Filtering by CNV to ExpressionNearMutations with loose cutoff of 1.0

#105 akmorrow13 closed 7 years ago
1
Added Filtering by CNV to ExpressionNearMutations with loose cutoff of 1.0

#104 akmorrow13 closed 7 years ago
0
Mutation ase distribution

#103 akmorrow13 closed 7 years ago
1
add MannWhitney tests

#102 akmorrow13 closed 7 years ago
2
Public docker image?

#101 sminot opened 7 years ago
2
Error while creating index

#100 riomario1 closed 4 years ago
3
Expression near mutations fix

#99 akmorrow13 closed 7 years ago
1
fixing off by one bug in BAM reader decodeSeqRC

#98 sbyma opened 7 years ago
1
Removed unused resources in MethylationAnalysis

#97 akmorrow13 closed 7 years ago
0
AnnotateVariants for Normal and Tumor RNA

#96 akmorrow13 closed 7 years ago
7
Tumor RNA file id fix in generatecases

#95 akmorrow13 closed 7 years ago
1
added Properties file for ExpressionNearMutations

#94 akmorrow13 closed 7 years ago
4
added assembly file for ExpressionByMutationCount

#93 akmorrow13 closed 7 years ago
0
Fixed Makefile for building snapxl-aligner

#92 taltman opened 7 years ago
1
Added in ExpressionNearMutations and MethylationAnalysis App

#91 akmorrow13 closed 7 years ago
2
'SNAPCommand exit' doesn't when previous job killed.

#90 taltman opened 7 years ago
0
Typo in Makefile for building snapxl

#89 taltman opened 7 years ago
0
Error message about long reads needs to be updated

#88 taltman opened 7 years ago
0
Error- GzipDataReader: inflate failed with -2

#87 MrOlm closed 4 years ago
5
can you help explain the question about the RAM used by snap

#86 wangzhenkeep opened 7 years ago
0
what is the command looks like for SNAP paired to use stdin/stdout

#85 wangzhenkeep closed 7 years ago
2
Documentation out of date

#84 MrOlm closed 7 years ago
4
Snap takes 3 hours to align two reads

#83 taltman closed 4 years ago
5
Build requires 188 GB of memory (fortunately not used, just allocated)

#82 tillea opened 7 years ago
1
Snap usage causes kernel 'soft lockup' bugs on Linux; odd performance profile

#81 taltman closed 4 years ago
1
SNAP doesn't support full FASTA/IUBMB/IUPAC sequence representation

#80 taltman closed 4 years ago
2
Odd output when building index from zcat command substitution

#79 taltman closed 4 years ago
5
Compiling on Ubuntu 16.10 fails

#78 lpryszcz closed 5 years ago
12
Further development?

#77 sklages closed 8 years ago
2
SNAP crashes when it tries to generate a BAM file with > 2GB header

#76 bolosky opened 8 years ago
0
The db is bigger and bigger but the aligenment time is shorter and shorter, why?

#75 wangzhenkeep closed 7 years ago
6
snap index not creating GenomeIndexHash%d files

#74 ericenns closed 8 years ago
2
Streaming input causing FASTQ parsing errors due to incorrect line breaks

#73 chapmanb closed 8 years ago
1
Inconsistent BAM output from identical inputs

#72 blahah opened 8 years ago
5
Fix compilation errors in C++11.

#71 SolalPirelli opened 8 years ago
2
Remove dead code

#70 SolalPirelli closed 7 years ago
3

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