search

4dn-dcic / pairix

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
MIT License
86 stars 14 forks source link

Error indexing a custom contact text file #39

Closed RXCoux closed 7 years ago

RXCoux commented 7 years ago

Hi, thanks a lot for making and maintaining all these very useful tools.

I have a custom made contact pairs file in the following format chr1 10000 20000 chr2 30000 50000 3.5

that I'm trying to index using pairix to load in cooler. I tried

pairix -s 1 -d 4 -b 2 -e 3 -u 5 -v 6 -T 3R.txt.gz

but I get

[get_intv] the following line cannot be parsed and skipped: chr3R 0 20000 chr3R 40000 60000 252

[ti_index_core] the indexes overlap or are out of bounds

It's the 1st line of my file and I don't really understand the error, my file only contains contacts for chr3R as I'm only interested in intra-chromosomal contacts.

3R.txt.gz

Could you please let me know if this error is reproducible or if I'm doing something wrong? Thanks in advance

SooLee commented 7 years ago

Hi, looks like your line is tab-delimited. Do you want to try without the -T option? The -T option assumes the file is space-delimited.

On Mon, Sep 11, 2017 at 11:38 AM, RXCoux notifications@github.com wrote:

Hi, thanks a lot for making and maintaining all these very useful tools.

I have a custom made contact pairs file in the following format chr1 10000 20000 chr2 30000 50000 3.5

that I'm trying to index using pairix to load in cooler. I tried

pairix -s 1 -d 4 -b 2 -e 3 -u 5 -v 6 -T 3R.txt.gz

but I get

[get_intv] the following line cannot be parsed and skipped: chr3R 0 20000 chr3R 40000 60000 252

[ti_index_core] the indexes overlap or are out of bounds

It's the 1st line of my file and I don't really understand the error, my file only contains contacts for chr3R as I'm only interested in intra-chromosomal contacts.

3R.txt.gz https://github.com/4dn-dcic/pairix/files/1293104/3R.txt.gz

Could you please let me know if this error is reproducible or if I'm doing something wrong? Thanks in advance

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/4dn-dcic/pairix/issues/39, or mute the thread https://github.com/notifications/unsubscribe-auth/AA63bHdK68VtBrZubCUJghjXS7zOy5ozks5shVPfgaJpZM4PTW63 .

RXCoux commented 7 years ago

Thanks that was a stupid mistake, my bad - it indeed worked