# Exact the sequence of chr1 in XAM.jl

**URL:** <https://discourse.julialang.org/t/exact-the-sequence-of-chr1-in-xam-jl/88163>\
**Category:** Biology, Health, and Medicine\
**Tags:** question\
**Created:** [October 3, 2022, 2:22pm UTC](https://discourse.julialang.org/t/exact-the-sequence-of-chr1-in-xam-jl/88163 "2022-10-03T14:22:17Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![zhangchunyong](https://avatars.discourse-cdn.com/v4/letter/z/d9b06d/32.png) [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Post date:** [October 3, 2022, 2:22pm UTC](https://discourse.julialang.org/t/exact-the-sequence-of-chr1-in-xam-jl/88163/1 "2022-10-03T14:22:17Z")

</div>

I only want to exact the sequence of chr1 not all.

```julia
using XAM
bamfile="..."
reader=open(BAM.Reader,bamfile)
for record in reader
    println(BAM.refname(record))
end

```

This returns all the chromosomes.I just want chr1.But I dont know how to do.  
I tried eachoverlap,but the function need start(1) and end(10000).

```julia
reader=open(BAM.Reader,bamfile,index=bamfile*".bai")
for record in eachoverlap(reader,"chr1",1:10000)
    println(BAM.refname(record))
end

```

and i also tried

```julia
reader.refseqlens
25-element Vector{Int64}:
 248956422
 133797422
 135086622
 133275309
 114364328
 107043718
 101991189
  90338345
  83257441
  80373285
  58617616
 242193529
  64444167
  46709983
  50818468
 198295559
 190214555
 181538259
 170805979
 159345973
 145138636
 138394717
     16569
 156040895
  57227415
for record in eachoverlap(reader,"chr1",1:248956422)
    println(BAM.refname(record))
end

```

It can return all of the chr1. I can only make it using eachoverlap(slow?).Are there any ways to make it faster? Thanks very much.

---

<div class="post-metadata">

**Author:** ![CiaranOMara](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/ciaranomara/32/2589_2.png) [@CiaranOMara](https://discourse.julialang.org/u/CiaranOMara)\
**Post date:** [October 17, 2022, 1:37pm UTC](https://discourse.julialang.org/t/exact-the-sequence-of-chr1-in-xam-jl/88163/2 "2022-10-17T13:37:51Z")

</div>

The `eachoverlap` method currently provides the best way to retrieve records.

You may want to use the recorded reference sequence length to set the end/right-hand position in the query.

```julia
reader = open(BAM.Reader, file_bam, index=file_bai)

chrom = "chr1"
idx = findfirst(isequal(chrom), reader.refseqnames)
refseqlen = reader.refseqlens[idx]

itr = eachoverlap(reader, Interval(chrom, 1, refseqlen)) # Equivalently eachoverlap(reader, chrom, 1:refseqlen)
records = collect(itr)

```

If working with a SAM file, you can find the reference sequence length in the header metadata.

```julia
idx = findfirst(reader.header.metainfo) do m
    SAM.tag(m) == "SQ" && m["SN"] == chrom
end
refseqlen = parse(Int, reader.header.metainfo[idx]["LN"])

```

I admit it’s worth adding short-hand `eachoverlap(reader::Reader, refname::String)` methods to XAM.