gatb / short_read_connector Goto Github PK

A boolean vector = one read file while in short read connector a query is a read set that can be composed of multiple read files.

I'm trying to update the Bioconda recipe for short-read-connector because it is a dependency of DiscoSnp, which I would like to incorporate into a workflow. However, the latest Bioconda recipe for short-read-connector is for v1.1.3, and is also build-blacklisted. Although the discosnp Bioconda recipe doesn't pin a specific version, it appears to require v1.2.0 because the DiscoSnpRad cookbook refers to short_read_connector_linker.sh.

I updated the Bioconda recipe and build.sh for short-read-connector (bioconda/bioconda-recipes#40889), but the build test on OS X is failing at the simple_test.

Unfortunately I'm not able to test the OS X build locally to troubleshoot.

Does your team possibly have some insight into what is happening? Thanks for your help.

Hello,

I have 15 technical control samples that I would like to use to filter reads occurring in real samples.
Basically I want to remove every reads with a high similarity with this control set of reads.

I initially concatenated all my files into two pairs and attempted to create the rconnector base. However, even with 200G of memory, this step does not pass. Do you have any recommendations ?

Dear Developpers,

I would like to use your this software but something is wrong with my data or command line.
I try to run short_read_connector_counter with the following line :
sh ./short_read_connector_counter.sh index -b hifi_reads.fasta.gz -i hifi_reads__my_counter_index.dumped

Where y input is a classical fasta file containing hifi reads. And the sd output tell me :

./short_read_connector_counter.sh: 10: ./short_read_connector_counter.sh: [[: not found
./short_read_connector_counter.sh: 15: ./short_read_connector_counter.sh: [[: not found
./short_read_connector_counter.sh: 29: ./short_read_connector_counter.sh: function: not found
short_read_connector_counter.sh - Compare reads from two read sets (distinct or not)
Version 1.2.0
Usage: sh short_read_connector_counter.sh [index/query]
./short_read_connector_counter.sh: 34: ./short_read_connector_counter.sh: Syntax error: "}" unexpected```

Thank for your help,
Best regards. 
Carole

1. Include the https://github.com/pierrepeterlongo/commet/blob/master/src/extract_reads.cpp tool in order to extract reads from .bv files.

2. Provide to way to create a .bv from a SRC counter or linker output. This would allow the creation of .bv files varying the threshold without the need to re-launch the whole process.