Error indexing a custom contact text file

[RXCoux]

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]

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.

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On Mon, Sep 11, 2017 at 11:38 AM, RXCoux ***@***.***> 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 <#39>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA63bHdK68VtBrZubCUJghjXS7zOy5ozks5shVPfgaJpZM4PTW63> .

[RXCoux]

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