Whisper

Whisper copied to clipboard

Segmentfault when aligning 25X e.coli single-end reads

8

Hi, whisper developers. I run the command `whisper ref/ref data1.fastq`, and whisper (released version 2.0.1) results in ``` ***** Preprocessing of reads ***** 100.0% Completing the preprocessing (could take a...

i-xiaohu

Binary file does not work

3

My computer doesn't have GCC 6.0+, so I downloaded the binary Whisper。 But，It seemed that the binary file did not work on linux。 ***** Stage 1. Reference sequence construction (direct)...

flystar233

Producing an index for a very large and very fragmented genome assembly

1

Dear developers, I would like to try out Whisper for mapping paired end short reads against a very large and fragmented genome assembly (100s of thousands of contigs). It is...

andreaswallberg

Hi, We have been testing Whisper on our large targeted capture data. The results look pretty encouraging as whisper takes only half the time taken by BWA-Mem. However, when you...

abolia

Output Mate Cigar and Mate Quality tags for each read

1

Hi, This is not a bug but I think it could be a good future improvement. It would be great to have tags related to mate quality and cigar (MQ...

abolia

Output not read-name sorted

2

Looks like in some circumstances the output is not sorted by read name. Technically speaking I think this is fine (the output is still valid .sam as far as I...

brendanofallon

Without the change build fails on `gcc-13` as: mapper/../common/defs.h:53:9: error: 'uint32_t' does not name a type 53 | typedef uint32_t ref_pos_t; | ^~~~~~~~ mapper/../common/defs.h:35:1: note: 'uint32_t' is defined in header...

trofi