Check that EOF_BLOCK gets written

Improve Slack link
Add doi to README
17 changed files with 309 additions and 167 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@ -7,7 +7,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

 ## [Unreleased]

-## [0.3.0]
+### Added
+- Added BAM.Reader index support for BAI object ([#56](https://github.com/BioJulia/XAM.jl/pull/56/files))
+- Added doi badge
+
+### Changed
+
+- Subtype from XAMReader and XAMWriter from common abstract types.
+- Subtype from XAMRecord.
+- Unified flag queries.
+
+## [0.3.1]
+
+### Changed
+
+- Upgraded to BioAlignments v3 ([#55](https://github.com/BioJulia/XAM.jl/pull/55))
+
+## [0.3.0] - 2022-10-10

 ## Added

@ -23,5 +39,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

 - `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26))

-[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...HEAD
+[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.1...HEAD
+[0.3.1]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...v0.3.1
 [0.3.0]: https://github.com/BioJulia/XAM.jl/compare/v0.2.8...v0.3.0
--- a/Project.toml
+++ b/Project.toml
@ -1,7 +1,7 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "0.3.0"
+version = "0.3.1"

 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
@ -17,7 +17,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 [compat]
 Automa = "0.7, 0.8"
 BGZFStreams = "0.3.1"
-BioAlignments = "2.2"
+BioAlignments = "3"
 BioGenerics = "0.1"
 BioSequences = "3"
 FormatSpecimens = "1.1"
--- a/README.md
+++ b/README.md
@ -2,6 +2,7 @@

 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Latest Release](https://img.shields.io/github/release/BioJulia/XAM.jl.svg)](https://github.com/BioJulia/XAM.jl/releases/latest)
+[![DOI](https://zenodo.org/badge/201858041.svg)](https://zenodo.org/badge/latestdoi/201858041)
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/XAM.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/XAM.jl/stable)
 [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/XAM.jl/dev/)
@ -65,4 +66,4 @@ Your logo will show up here with a link to your website.


 ## Questions?
-If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.slack.com/channels/biology), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
--- a/docs/src/index.md
+++ b/docs/src/index.md
@ -64,4 +64,4 @@ Your logo will show up here with a link to your website.


 ## Questions?
-If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.slack.com/channels/biology), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
--- a/src/XAM.jl
+++ b/src/XAM.jl
@ -1,29 +1,17 @@
 module XAM

+using BioGenerics
+import BioGenerics: isfilled #Note: used by `ismapped`.
+
 export
    SAM,
    BAM

-"""
-    flag(record::Union{SAM.Record, BAM.Record})::UInt16
-
-Get the bitwise flags of `record`. The returned value is a `UInt16` of each flag
-being OR'd together. The possible flags are:
+abstract type XAMRecord end
+abstract type XAMReader <: BioGenerics.IO.AbstractReader end
+abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end

-    0x0001 template having multiple segments in sequencing
-    0x0002 each segment properly aligned according to the aligner
-    0x0004 segment unmapped
-    0x0008 next segment in the template unmapped
-    0x0010 SEQ being reverse complemented
-    0x0020 SEQ of the next segment in the template being reverse complemented
-    0x0040 the first segment in the template
-    0x0080 the last segment in the template
-    0x0100 secondary alignment
-    0x0200 not passing filters, such as platform/vendor quality controls
-    0x0400 PCR or optical duplicate
-    0x0800 supplementary alignment
-"""
-function flag end
+include("flags.jl")

 include("sam/sam.jl")
 include("bam/bam.jl")
--- a/src/bam/bam.jl
+++ b/src/bam/bam.jl
@ -6,7 +6,8 @@ module BAM
 using BioGenerics
 using GenomicFeatures
 using XAM.SAM
-import ..XAM: flag
+import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
+	ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.

 import BGZFStreams
 import BioAlignments
--- a/src/bam/reader.jl
+++ b/src/bam/reader.jl
@ -8,9 +8,9 @@ Create a data reader of the BAM file format.

 # Arguments
 * `input`: data source
-* `index=nothing`: filepath to a random access index (currently *bai* is supported)
+* `index=nothing`: filepath to a random access index (currently *bai* is supported) or BAI object
 """
-mutable struct Reader{T} <: BioGenerics.IO.AbstractReader
+mutable struct Reader{T} <: XAMReader
    stream::BGZFStreams.BGZFStream{T}
    header::SAM.Header
    start_offset::BGZFStreams.VirtualOffset
@ -28,13 +28,8 @@ function BioGenerics.IO.stream(reader::Reader)
 end

 function Reader(input::IO; index=nothing)
-    if isa(index, AbstractString)
-        index = BAI(index)
-    elseif index != nothing
-        error("unrecognizable index argument")
-    end
    reader = init_bam_reader(input)
-    reader.index = index
+    reader.index = init_bam_index(index)
    return reader
 end

@ -125,6 +120,11 @@ function init_bam_reader(input::IO)
    return init_bam_reader(BGZFStreams.BGZFStream(input))
 end

+init_bam_index(index::AbstractString) = BAI(index)
+init_bam_index(index::BAI) = index
+init_bam_index(index::Nothing) = nothing
+init_bam_index(index) = error("unrecognizable index argument")
+
 function _read!(reader::Reader, record)
    unsafe_read(
        reader.stream,
--- a/src/bam/record.jl
+++ b/src/bam/record.jl
@ -6,7 +6,7 @@

 Create an unfilled BAM record.
 """
-mutable struct Record
+mutable struct Record <: XAMRecord
    # fixed-length fields (see BMA specs for the details)
    block_size::Int32
    refid::Int32
@ -137,37 +137,6 @@ function hasflag(record::Record)
    return isfilled(record)
 end

-"""
-    ismapped(record::Record)::Bool
-
-Test if `record` is mapped.
-"""
-function ismapped(record::Record)::Bool
-    return flag(record) & SAM.FLAG_UNMAP == 0
-end
-
-"""
-    isprimary(record::Record)::Bool
-
-Test if `record` is a primary line of the read.
-
-This is equivalent to `flag(record) & 0x900 == 0`.
-"""
-function isprimary(record::Record)::Bool
-    return flag(record) & 0x900 == 0
-end
-
-"""
-    ispositivestrand(record::Record)::Bool
-
-Test if `record` is aligned to the positive strand.
-
-This is equivalent to `flag(record) & 0x10 == 0`.
-"""
-function ispositivestrand(record::Record)::Bool
-    flag(record) & 0x10 == 0
-end
-
 """
    refid(record::Record)::Int

@ -253,15 +222,6 @@ function hasrightposition(record::Record)
    return isfilled(record) && ismapped(record)
 end

-"""
-    isnextmapped(record::Record)::Bool
-
-Test if the mate/next read of `record` is mapped.
-"""
-function isnextmapped(record::Record)::Bool
-    return isfilled(record) && (flag(record) & SAM.FLAG_MUNMAP == 0)
-end
-
 """
    nextrefid(record::Record)::Int

@ -430,27 +390,11 @@ end
 Get the alignment of `record`.
 """
 function alignment(record::Record)::BioAlignments.Alignment
-    checkfilled(record)
-    if !ismapped(record)
-        return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
+    if ismapped(record)
+        return BioAlignments.Alignment(cigar(record), 1, position(record))
    end
-    seqpos = 0
-    refpos = position(record) - 1
-    anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, BioAlignments.OP_START)]
-    for (op, len) in zip(cigar_rle(record)...)
-        if BioAlignments.ismatchop(op)
-            seqpos += len
-            refpos += len
-        elseif BioAlignments.isinsertop(op)
-            seqpos += len
-        elseif BioAlignments.isdeleteop(op)
-            refpos += len
-        else
-            error("operation $(op) is not supported")
-        end
-        push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, op))
-    end
-    return BioAlignments.Alignment(anchors)
+
+    return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
 end

 function hasalignment(record::Record)
--- a/src/bam/writer.jl
+++ b/src/bam/writer.jl
@ -10,7 +10,7 @@ Create a data writer of the BAM file format.
 * `output`: data sink
 * `header`: SAM header object
 """
-mutable struct Writer <: BioGenerics.IO.AbstractWriter
+mutable struct Writer <: XAMWriter
    stream::BGZFStreams.BGZFStream
 end

--- a/src/flags.jl
+++ b/src/flags.jl
@ -0,0 +1,226 @@
+# Flags
+# =========
+#
+
+"""
+    flag(record::XAMRecord})::UInt16
+
+Get the bitwise flags of `record`.
+The returned value is a `UInt16` of each flag being OR'd together.
+The possible flags are:
+
+    0x0001 template having multiple segments in sequencing
+    0x0002 each segment properly aligned according to the aligner
+    0x0004 segment unmapped
+    0x0008 next segment in the template unmapped
+    0x0010 SEQ being reverse complemented
+    0x0020 SEQ of the next segment in the template being reverse complemented
+    0x0040 the first segment in the template
+    0x0080 the last segment in the template
+    0x0100 secondary alignment
+    0x0200 not passing filters, such as platform/vendor quality controls
+    0x0400 PCR or optical duplicate
+    0x0800 supplementary alignment
+"""
+
+function flag end
+
+# Bitwise flags (or FLAG).
+for (name, bits, doc) in [
+        (:PAIRED,        UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
+        (:PROPER_PAIR,   UInt16(0x002), "the read is mapped in a proper pair"                                       ),
+        (:UNMAP,         UInt16(0x004), "the read itself is unmapped; conflictive with FLAG_PROPER_PAIR"            ),
+        (:MUNMAP,        UInt16(0x008), "the mate is unmapped"                                                      ),
+        (:REVERSE,       UInt16(0x010), "the read is mapped to the reverse strand"                                  ),
+        (:MREVERSE,      UInt16(0x020), "the mate is mapped to the reverse strand"                                  ),
+        (:READ1,         UInt16(0x040), "this is read1"                                                             ),
+        (:READ2,         UInt16(0x080), "this is read2"                                                             ),
+        (:SECONDARY,     UInt16(0x100), "not primary alignment"                                                     ),
+        (:QCFAIL,        UInt16(0x200), "QC failure"                                                                ),
+        (:DUP,           UInt16(0x400), "optical or PCR duplicate"                                                  ),
+        (:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment"                                                   ),]
+    @assert bits isa UInt16 "The bits must be of type UInt16."
+    sym = Symbol("FLAG_", name)
+    docstring = """    $sym
+    SAM/BAM flag: $doc
+
+    See also: [`flag`](@ref)
+    """
+    @eval begin
+        @doc $(docstring) const $(sym) = $(bits)
+    end
+end
+
+"""
+    ispaired(record::XAMRecord)::Bool
+
+Query whether the `record`'s template has multiple segments in sequencing.
+"""
+function ispaired(record::XAMRecord)::Bool
+    return flag(record) & FLAG_PAIRED == FLAG_PAIRED
+end
+
+"""
+    isproperpair(record::XAMRecord)::Bool
+
+Query whether each segment of the `record`'s template properly aligned according to the aligner.
+"""
+function isproperpair(record::XAMRecord)::Bool
+    return flag(record) & PROPER_PAIR == PROPER_PAIR
+end
+
+"""
+    isunmapped(record::XAMRecord)::Bool
+
+Query whether the `record` is unmapped.
+"""
+function isunmapped(record::XAMRecord)::Bool
+    return flag(record) & FLAG_UNMAP == FLAG_UNMAP
+end
+
+"""
+    ismapped(record::XAMRecord)::Bool
+
+Query whether the `record` is mapped.
+"""
+function ismapped(record::XAMRecord)::Bool
+    # return flag(record) & FLAG_UNMAP == 0
+    return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
+end
+
+"""
+    ismateunmapped(record::XAMRecord)::Bool
+
+Query whether the `record`'s mate is unmapped.
+"""
+function ismateunmapped(record::XAMRecord)::Bool
+    return flag(record) & FLAG_MUNMAP == FLAG_MUNMAP
+end
+
+"""
+    isnextmapped(record::XAMRecord)::Bool
+
+Test if the mate/next read of `record` is mapped.
+"""
+function isnextmapped(record::XAMRecord)::Bool
+    return flag(record) & FLAG_MUNMAP == 0
+end
+
+"""
+    isreverse(record::XAMRecord)::Bool
+
+Query whether the `record` is mapped to the reverse strand.
+"""
+function isreverse(record::XAMRecord)::Bool
+    return flag(record) & FLAG_REVERSE == FLAG_REVERSE
+end
+
+"""
+    isforward(record::XAMRecord)::Bool
+
+Query whether the `record` is mapped to the forward strand.
+"""
+function isforward(record::XAMRecord)::Bool
+    return flag(record) & FLAG_REVERSE == 0
+end
+
+"""
+    ispositivestrand(record::XAMRecord)::Bool
+
+Query whether `record` is aligned to the positive strand.
+"""
+function ispositivestrand(record::XAMRecord)::Bool
+    return isforward(record)
+end
+
+"""
+    ispositivestrand(record::XAMRecord)::Bool
+
+Query whether `record` is aligned to the negative strand.
+"""
+function isnegativestrand(record::XAMRecord)::Bool
+    return isreverse(record)
+end
+
+"""
+    ismatereverse(record::XAMRecord)::Bool
+
+Query whether the `record`'s mate is mapped to the reverse strand.
+"""
+function ismatereverse(record::XAMRecord)::Bool
+    return flag(record) & FLAG_MREVERSE == FLAG_MREVERSE
+end
+
+"""
+    isread1(record::XAMRecord)::Bool
+
+Query whether the `record` is read1.
+"""
+function isread1(record::XAMRecord)::Bool
+    return flag(record) & FLAG_READ1 == FLAG_READ1
+end
+
+"""
+    isread2(record::XAMRecord)::Bool
+
+Query whether the `record` is read2.
+"""
+function isread2(record::XAMRecord)::Bool
+    return flag(record) & FLAG_READ2 == FLAG_READ2
+end
+
+"""
+    issecondaryalignment(record::XAMRecord)::Bool
+
+Query whether the `record` is a secondary alignment.
+"""
+function issecondaryalignment(record::XAMRecord)::Bool
+    return flag(record) & FLAG_SECONDARY == FLAG_SECONDARY
+end
+
+"""
+    isprimaryalignment(record::XAMRecord)::Bool
+
+Query whether the `record` is the primary alignment.
+"""
+function isprimaryalignment(record::XAMRecord)::Bool
+    return flag(record) & FLAG_SECONDARY == 0
+end
+
+"""
+    isqcfail(record::XAMRecord)::Bool
+
+Query whether the `record` did not pass filters, such as platform/vendor quality controls.
+"""
+function isqcfail(record::XAMRecord)::Bool
+    return flag(record) & FLAG_QCFAIL == FLAG_QCFAIL
+end
+
+"""
+    isduplicate(record::XAMRecord)::Bool
+
+Query whether the `record` is a PCR or optical duplicate.
+"""
+function isduplicate(record::XAMRecord)::Bool
+    return flag(record) & FLAG_DUP == FLAG_DUP
+end
+
+"""
+    issupplementaryalignment(record::XAMRecord)::Bool
+
+Query whether the `record` is a supplementary alignment.
+"""
+function issupplementaryalignment(record::XAMRecord)::Bool
+    return flag(record) & FLAG_SUPPLEMENTARY == FLAG_SUPPLEMENTARY
+end
+
+"""
+    isprimary(record::XAMRecord)::Bool
+
+Query whether `record` is a primary line of the read.
+
+This is equivalent to `flag(record) & 0x900 == 0`.
+"""
+function isprimary(record::XAMRecord)::Bool
+    return flag(record) & 0x900 == 0
+end
--- a/src/sam/flags.jl
+++ b/src/sam/flags.jl
@ -1,29 +0,0 @@
-# SAM Flags
-# =========
-#
-# Bitwise flags (or FLAG).
-
-for (name, bits, doc) in [
-        (:PAIRED,        UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
-        (:PROPER_PAIR,   UInt16(0x002), "the read is mapped in a proper pair"                                       ),
-        (:UNMAP,         UInt16(0x004), "the read itself is unmapped; conflictive with SAM.FLAG_PROPER_PAIR"        ),
-        (:MUNMAP,        UInt16(0x008), "the mate is unmapped"                                                      ),
-        (:REVERSE,       UInt16(0x010), "the read is mapped to the reverse strand"                                  ),
-        (:MREVERSE,      UInt16(0x020), "the mate is mapped to the reverse strand"                                  ),
-        (:READ1,         UInt16(0x040), "this is read1"                                                             ),
-        (:READ2,         UInt16(0x080), "this is read2"                                                             ),
-        (:SECONDARY,     UInt16(0x100), "not primary alignment"                                                     ),
-        (:QCFAIL,        UInt16(0x200), "QC failure"                                                                ),
-        (:DUP,           UInt16(0x400), "optical or PCR duplicate"                                                  ),
-        (:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment"                                                   ),]
-    @assert bits isa UInt16 "The bits must be of type UInt16."
-    sym = Symbol("FLAG_", name)
-    docstring = """    $sym
-    SAM/BAM flag: $doc
-
-    See also: [`flag`](@ref)
-    """
-    @eval begin
-        @doc $(docstring) const $(sym) = $(bits)
-    end
-end
--- a/src/sam/reader.jl
+++ b/src/sam/reader.jl
@ -1,7 +1,7 @@
 # SAM Reader
 # =========

-mutable struct Reader{S <: TranscodingStream} <: BioGenerics.IO.AbstractReader
+mutable struct Reader{S <: TranscodingStream} <: XAMReader
    state::State{S}
    header::Header
 end
--- a/src/sam/record.jl
+++ b/src/sam/record.jl
@ -1,7 +1,7 @@
 # SAM Record
 # ==========

-mutable struct Record
+mutable struct Record <: XAMRecord
    # Data and filled range.
    data::Vector{UInt8}
    filled::UnitRange{Int} # Note: Specifies the data in use.
@ -159,26 +159,6 @@ function hasflag(record::Record)
    return isfilled(record)
 end

-"""
-    ismapped(record::Record)::Bool
-
-Test if `record` is mapped.
-"""
-function ismapped(record::Record)::Bool
-    return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
-end
-
-"""
-    isprimary(record::Record)::Bool
-
-Test if `record` is a primary line of the read.
-
-This is equivalent to `flag(record) & 0x900 == 0`.
-"""
-function isprimary(record::Record)::Bool
-    return flag(record) & 0x900 == 0
-end
-
 """
    refname(record::Record)::String

@ -227,15 +207,6 @@ function hasrightposition(record::Record)
    return hasposition(record) && hasalignment(record)
 end

-"""
-    isnextmapped(record::Record)::Bool
-
-Test if the mate/next read of `record` is mapped.
-"""
-function isnextmapped(record::Record)::Bool
-    return isfilled(record) && (flag(record) & FLAG_MUNMAP == 0)
-end
-
 """
    nextrefname(record::Record)::String

--- a/src/sam/sam.jl
+++ b/src/sam/sam.jl
@ -11,7 +11,8 @@ import BioGenerics.Exceptions: missingerror
 import BioGenerics.Automa: State
 import BioSequences
 import TranscodingStreams: TranscodingStreams, TranscodingStream
-import ..XAM: flag
+import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
+    ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.

 using Printf: @sprintf

@ -48,7 +49,6 @@ function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{I
 end


-include("flags.jl")
 include("metainfo.jl")
 include("record.jl")
 include("header.jl")
--- a/src/sam/writer.jl
+++ b/src/sam/writer.jl
@ -10,7 +10,7 @@ Create a data writer of the SAM file format.
 * `output`: data sink
 * `header=Header()`: SAM header object
 """
-mutable struct Writer <: BioGenerics.IO.AbstractWriter
+mutable struct Writer <: XAMWriter
    stream::IO

    function Writer(output::IO, header::Header=Header())
--- a/test/test_bam.jl
+++ b/test/test_bam.jl
@ -79,10 +79,10 @@
        @test BAM.flag(record) === UInt16(16)
        @test BAM.cigar(record) == "27M1D73M"
        @test BAM.alignment(record) == Alignment([
-            AlignmentAnchor(  0,   1, OP_START),
-            AlignmentAnchor( 27,  28, OP_MATCH),
-            AlignmentAnchor( 27,  29, OP_DELETE),
-            AlignmentAnchor(100, 102, OP_MATCH)])
+            AlignmentAnchor(  0,   1,   0, OP_START),
+            AlignmentAnchor( 27,  28,  27, OP_MATCH),
+            AlignmentAnchor( 27,  29,  28, OP_DELETE),
+            AlignmentAnchor(100, 102, 101, OP_MATCH)])
        @test record["XG"] == 1
        @test record["XM"] == 5
        @test record["XN"] == 0
@ -209,6 +209,14 @@
                close(reader)
                close(writer)

+
+                # Check that EOF_BLOCK gets written.
+                nbytes = filesize(path)
+                @test BAM.BGZFStreams.EOF_BLOCK == open(path) do io
+                    seek(io, nbytes - length(BAM.BGZFStreams.EOF_BLOCK))
+                    read(io)
+                end
+
                reader = open(BAM.Reader, path)

                @test header(reader) == header_original
@ -241,6 +249,21 @@

    end

+    @testset "BAI" begin
+
+        filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
+
+        index = BAM.BAI(filepath * ".bai")
+        reader = open(BAM.Reader, filepath, index=index)
+
+        @test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
+
+        close(reader)
+
+        @test_throws ErrorException open(BAM.Reader, filepath, index=1234)
+
+    end
+
    @testset "Random access" begin
        filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
        reader = open(BAM.Reader, filepath, index=filepath * ".bai")
--- a/test/test_sam.jl
+++ b/test/test_sam.jl
@ -104,10 +104,10 @@
        @test SAM.flag(record) == 16
        @test SAM.cigar(record) == "27M1D73M"
        @test SAM.alignment(record) == Alignment([
-            AlignmentAnchor(  0,   1, OP_START),
-            AlignmentAnchor( 27,  28, OP_MATCH),
-            AlignmentAnchor( 27,  29, OP_DELETE),
-            AlignmentAnchor(100, 102, OP_MATCH)])
+            AlignmentAnchor(  0,   1,   0, OP_START),
+            AlignmentAnchor( 27,  28,  27, OP_MATCH),
+            AlignmentAnchor( 27,  29,  28, OP_DELETE),
+            AlignmentAnchor(100, 102, 101, OP_MATCH)])
        @test record["XG"] == 1
        @test record["XM"] == 5
        @test record["XN"] == 0
Author	SHA1	Message	Date
Ciarán O'Mara	560a5cd8df	Check that EOF_BLOCK gets written	1 year ago
Ciarán O'Mara	10c1aacd4d	Improve Slack link	1 year ago
Ciarán O'Mara	cc5f21b854	Add doi to README	1 year ago
Ciarán O'Mara	9a9f2c1f5a	Fun with flags Implements flag queries.	1 year ago
Ciarán O'Mara	0d1eec3ed3	Subtype from XAMRecord	1 year ago
Ciarán O'Mara	8151d877e7	Subtype from XAMReader and XAMWriter	1 year ago
Ciarán O'Mara	50039e749f	Update CHANGELOG	2 years ago
Ciarán O'Mara	8272cea71e	Merge pull request #56 from jonathanBieler/bam_index_method Added method for handling different bam index types.	2 years ago
Ciarán O'Mara	bda532e2ce	Merge branch 'master' into develop	2 years ago
Ciarán O'Mara	22f939ffbe	Merge pull request #57 from BioJulia/release/0.3.1 Release v0.3.1	2 years ago
Thomas A. Christensen II	fe83a749d2	Update CHANGELOG for v0.3.1	2 years ago
Thomas A. Christensen II	1c57e9b0e2	Bump version number in Project.toml to 0.3.1	2 years ago
Thomas A. Christensen II	e2b22becf4	Merge pull request #55 from MillironX/feature/bioalignments-3	2 years ago
Jonathan Bieler	286e271e91	update docstring	2 years ago
Jonathan Bieler	93a6b60d26	added method for handling different bam index types	2 years ago
Thomas A. Christensen II	32e3213ee8	Update CHANGELOG	2 years ago
Thomas A. Christensen II	f7b9d9fa75	Update tests to use new AlignmentAnchor structure	2 years ago
Thomas A. Christensen II	9720fd0fcd	Bump BioAlignments version compat to 3	2 years ago
Thomas A. Christensen II	e6f542a368	Change alignment getter for BAM.Record to use existing cigar constructor Rather than keep a copy of the BioAlignments cigar constructor embedded in this function, have it call the existing constructor. There may be performance implications for using `cigar` instead of `cigar_rle`, but having a second copy of the constructor here is an antipattern if I've ever seen one, so prioritise stable code over performant code.	2 years ago