Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field?

you can make it faster with grep -wFf qnames.list reads.sam On Mon, Aug 18, 2014 at 8:32 AM, csoeder wrote: > Hi! I would like to query a sam/bam file by its qname field. Can this be done > with samtools? I haven't seen anything like it in the documentation. I've > tried > > grep -f qnames.list

[Samtools-help] tweak_overlap_quality

Is it true that tweak_overlap_quality is now used by default in mpileup for samtools version 1 and that was not the case in 0.1.19? thanks, -Brent -- Want excitement? Manually upgrade your production database. When you wan

[Samtools-help] crai

Hi, is there any documentation on the CRAI format beyond the numbered list in this file: https://samtools.github.io/hts-specs/CRAMv3.pdf I have a .crai with a negative alignment span. The row looks like this: 22251 -2147483648 14896634174 936 628560 I'm wondering what that

Re: [Samtools-help] crai

thanks for the quick fix. On Thu, May 11, 2017 at 3:24 AM, James Bonfield wrote: > On Wed, May 10, 2017 at 11:34:46AM -0600, Brent Pedersen wrote: >> I have a .crai with a negative alignment span. The row looks like this: >> >> 22251 -2147483648 148966341

[Samtools-help] hts_set_threads for n==1

hi, it seems that if I call without l hts_set_threads, I get, as expected 100% cpu for a process that is reading a BAM or CRAM. If I call it with nthreads = 1, I get 100% cpu. If I call it with nthreads = 2, I get 300% cpu. Is there a way to get it to use 2 cpus? thanks, -Brent -

Re: [Samtools-help] hts_set_threads for n==1

On Tue, Aug 29, 2017 at 2:58 AM, James Bonfield wrote: > On Sun, Aug 27, 2017 at 12:08:16PM -0600, Brent Pedersen wrote: >> hi, it seems that if I call without l hts_set_threads, I get, as >> expected 100% cpu for a process that is reading a BAM or CRAM. >> If I call it wit

[Samtools-help] csi index while bgzipping

based on the API: int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped); and a quick look at the code, it looks like I might be able to create a .csi index while writing a bgzip output. Is that correct? basically, if I've just written a line/interval to fp

Re: [Samtools-help] csi index while bgzipping

just to follow up in case anyone else wonders about this... it seems to work fine to do essentially as described to allow indexing while writing. On Tue, Sep 19, 2017 at 9:55 AM, Brent Pedersen wrote: > based on the API: > int hts_idx_push(hts_idx_t *idx, int tid, int beg, i

[Samtools-help] crai

Hi, I have a tool that parses crai and a user has 2 adjacent lines like this: 1 243185013 436216775145505 611 180875 1 10173 13477 16775327057 623 260625 note that 10173 follows 243185013. Is there any way this can occur for a valid crai? thanks, -Brent

[Samtools-help] CSI stats bins

With bam/tabix, we can recognize the stats bin in index 37450 It is not documented how to find this bin for CSI which can have real data in 37450. What is the way to find it? thanks, -Brent -- Check out the vibrant tech

Re: [Samtools-help] CSI stats bins

On Thu, Dec 14, 2017 at 1:57 PM, John Marshall wrote: > On 15 Dec 2017, Brent Pedersen wrote: >> With bam/tabix, we can recognize the stats bin in index 37450 >> >> It is not documented how to find this bin for CSI which can have real >> data in 37450. > > Ther

[Samtools-help] REF_CACHE

Hi, I've been working more with crams lately and in some cases, it seems the default behavior of htslib is to automatically start downloading reference files locally even though I have not set REF_CACHE or REF_PATH. This is deep in a complex pipeline behind several layers of abstraction, but I thin

Re: [Samtools-help] REF_CACHE

On Thu, Feb 8, 2018 at 11:13 AM, James Bonfield wrote: > On Thu, Feb 08, 2018 at 09:32:00AM -0700, Brent Pedersen wrote: >> I've been working more with crams lately and in some cases, it seems >> the default behavior of htslib is to automatically start downloading >> re

Re: [Samtools-help] REF_CACHE

, I had to do: wget -q https://raw.githubusercontent.com/samtools/samtools/develop/misc/seq_cache_populate.pl perl seq_cache_populate.pl -root $(pwd)/cache ${fasta} export REF_PATH=$(pwd)/cache/%2s/%2s/%s:http://www.ebi.ac.uk/ena/cram/md5/%s export REF_CACHE=xx -Brent On Wed, Feb 28, 2018 at

[Samtools-help] read sequence

Hi, I want to store a minimal representation of an alignment (more minimal than CRAM). I thought I could save the position, cigar, and MD and be able to reconstruct the read sequence, but the MD (IIUC) allows reconstructing the reference from the read. Is there something exposed in the current hts

Re: [Samtools-help] read sequence

On Mon, Oct 22, 2018, 7:05 AM James Bonfield On Fri, Oct 19, 2018 at 04:30:33PM -0600, Brent Pedersen wrote: > > I want to store a minimal representation of an alignment (more minimal > > than CRAM). > > I thought I could save the position, cigar, and MD and be able to &

[Samtools-help] reset sam/bam/cram iterator

Hi, if I use sam_read1 to iterate over a bam in order, is there a simple way to reset the iterator (the htsFile pointer) to the start of the file (after the header)? Or should I just close and re-open? thanks, -B ___ Samtools-help mailing list Samtool