find() instead of findall() in hts-files.md

[aalexandersson]

There seems to be a typo in the file BioAlignments.jl/docs/src/hts-files.md

Expected Behavior

I expected this code to work in Julia 1.1.0:

find(header(reader), "SQ")

I suggest to use findall() instead of find(), like this:

findall(header(reader), "SQ")

Current Behavior

The current code gives this error:

UndefVarError: find not defined

The suggested change instead results in this:

2-element Array{BioAlignments.SAM.MetaInfo,1}:
 BioAlignments.SAM.MetaInfo:
    tag: SQ
  value: SN=chr1 LN=1575
 BioAlignments.SAM.MetaInfo:
    tag: SQ
  value: SN=chr2 LN=1584

Possible Solution / Implementation

Replace find() with findall() for Julia 1.x.

Steps to Reproduce (for bugs)

Download the file ex1_header.sam, then run this code in Atom

using BioAlignments
reader = open(SAM.Reader, "ex1_header.sam");
find(header(reader), "SQ")

Context

Obviously, I am a Julia beginner. I am trying to learn how to read a SAM file and a BAM file using BioAlignments. The documentation refers to "data.sam" and "data.bam" which are only generic hypothetical files. I would like to have a fully reproducible example with a real file instead such as ex1_header.sam from https://github.com/BioJulia/BioFmtSpecimens/tree/master/SAM

I tried to add Bio but received this error message:

(v1.1) pkg> add Bio
  Updating registry at `C:\Users\aalexandersson\.julia\registries\General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package Bio [3637df68]:
 Bio [3637df68] log:
 ├─possible versions are: [0.1.0, 0.2.0-0.2.3, 0.3.0, 0.4.0-0.4.7] or uninstalled
 ├─restricted to versions * by an explicit requirement, leaving only versions [0.1.0, 0.2.0-0.2.3, 0.3.0, 0.4.0-0.4.7]
 └─restricted by julia compatibility requirements to versions: uninstalled - no versions left

Then I successfully installed BioAlignments individually.

Your Environment

julia> versioninfo()
Julia Version 1.1.0
Commit 80516ca202 (2019-01-21 21:24 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM) i7 CPU         870  @ 2.93GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, nehalem)
Environment:
  JULIA_EDITOR = "C:\Users\aalexandersson\AppData\Local\atom\app-1.29.0\atom.exe" -a
  JULIA_NUM_THREADS = 4

(v1.1) pkg> status
    Status `C:\Users\aalexandersson\.julia\environments\v1.1\Project.toml`
  [c52e3926] Atom v0.7.14
  [9e28174c] BinDeps v0.8.10
  [00701ae9] BioAlignments v1.0.0
  [37cfa864] BioCore v2.0.5
  [7e6ae17a] BioSequences v1.1.0
  [159f3aea] Cairo v0.5.6
  [34da2185] Compat v1.5.1
  [a93c6f00] DataFrames v0.17.0
  [186bb1d3] Fontconfig v0.2.0
  [c91e804a] Gadfly v1.0.1
  [c43c736e] Genie v0.1.0 #master (https://github.com/essenciary/Genie.jl)
  [e5e0dc1b] Juno v0.5.4
  [ce6b1742] RDatasets v0.6.1
  [b8865327] UnicodePlots v1.0.1