SAMReader

all_records deprecated alias all_records = allRecords: Undocumented in source.
fetch alias fetch = query: fetch is provided as a PySAM compatible synonym for query
n_targets alias n_targets = nTargets: Undocumented in source.
targetLen alias targetLen = targetLength: Undocumented in source.
targetLens alias targetLens = targetLengths: Undocumented in source.
target_id alias target_id = targetId: Undocumented in source.
target_len alias target_len = targetLength: Undocumented in source.
target_lens alias target_lens = targetLengths: Undocumented in source.
target_names alias target_names = targetNames: Undocumented in source.

Functions

allRecords auto allRecords(): Return an InputRange representing all records in the SAM/BAM/CRAM
opDollar OffsetType opDollar(): Array-end $ indexing hack courtesy of Steve Schveighoffer https://forum.dlang.org/post/rl7a56$nad$1@digitalmars.com
opIndex auto opIndex(string[] regions): opIndex with a list of string regions bam[["chr1:1-3","chr2:4-50"]]
opIndex auto opIndex(string contig, Interval!cs coords): opIndex with a string contig and an Interval bam["chr1", ZBHO(1,3)]
opIndex auto opIndex(int tid, Interval!cs coords): opIndex with an int tid and an Interval bam[0, ZBHO(1,3)]
opIndex auto opIndex(string contig, Coordinate!bs pos): opIndex with a string contig and a Coordinate bam["chr1", ZB(1)]
opIndex auto opIndex(int tid, Coordinate!bs pos): opIndex with an int tid and a Coordinate bam[0, ZB(1)]
opIndex deprecated auto opIndex(string tid, Coordinate!bs pos1, Coordinate!bs pos2): opIndex with a string contig and two Coordinates bam["chr1", ZB(1), ZB(3)]
opIndex deprecated auto opIndex(int tid, Coordinate!bs pos1, Coordinate!bs pos2): opIndex with an int tid and two Coordinates bam[0, ZB(1), ZB(3)]
opIndex auto opIndex(string ctg, OffsetType endoff): opIndex with a string contig and an Offset bam["chr1",$-2]
opIndex auto opIndex(int tid, OffsetType endoff): opIndex with an int tid and an Offset bam[0,$-2]
opIndex auto opIndex(string ctg, Tuple!(Coordinate!bs, OffsetType) coords): opIndex with a string contig and a Coordinate and Offset bam["chr1",ZB(1) .. $]
opIndex auto opIndex(int tid, Tuple!(Coordinate!bs, OffsetType) coords): opIndex with an int tid and a Coordinate and Offset bam[0,ZB(1) .. $]
opIndex auto opIndex(string ctg, Tuple!(OffsetType, OffsetType) coords): opIndex two Offsets i.e fai["chrom1", $-2 .. $]
opIndex auto opIndex(int tid, Tuple!(OffsetType, OffsetType) coords): opIndex with an int tid and a Coordinate and Offset bam[0,ZB(1) .. $]
opSlice auto opSlice(Coordinate!bs start, Coordinate!bs end): opSlice with two Coordinates [ZB(1) .. ZB(3)]
opSlice auto opSlice(Coordinate!bs start, OffsetType off): opSlice as Coordinate and an offset i.e [ZB(2) .. $]
opSlice auto opSlice(OffsetType start, OffsetType end): opSlice as two offset i.e [$-2 .. $]
query auto query(string chrom, Interval!cs coords)
auto query(int tid, Interval!cs coords)
auto query(string[] regions): Query a region and return matching alignments as InputRange
targetId deprecated int targetId(string name): reference contig name to integer id
targetLength deprecated uint targetLength(int target): length of specific reference sequence by number (tid)

Properties

nTargets deprecated int nTargets [@property getter]: number of reference sequences; from bam_hdr_t
targetLengths deprecated uint[] targetLengths [@property getter]: lengths of the reference sequences
targetNames deprecated string[] targetNames [@property getter]: names of the reference sequences

Structs

AllRecordsRange struct AllRecordsRange: Iterate through all records in the SAM
RecordRange struct RecordRange: Iterate over records falling within a queried region
RecordRangeMulti struct RecordRangeMulti: Iterate over records falling within queried regions using a RegionList

Variables

filename string filename;: filename; as usable from D
header SAMHeader header;: header struct

Examples

import dhtslib.sam;
import htslib.hts_log : hts_log_info;
import std.path : buildPath, dirName;
import std.string : fromStringz;
import std.array : array; 

hts_set_log_level(htsLogLevel.HTS_LOG_WARNING);
hts_log_info(__FUNCTION__, "Testing SAMFile & SAMRecord");
hts_log_info(__FUNCTION__, "Loading test file");
auto sam = SAMFile(buildPath(dirName(dirName(dirName(dirName(__FILE__)))),"htslib","test","auxf#values.sam"), 0);
auto sam2 = SAMWriter("/tmp/test.bam", sam.header);
auto readrange = sam.allRecords;
hts_log_info(__FUNCTION__, "Getting read 1");
assert(readrange.empty == false);
auto read = readrange.front();

// writeln(read.sequence);
assert(read.sequence=="GCTAGCTCAG");
assert(sam.allRecords.array.length == 2);
sam2.write(read);
destroy(sam2);


// testing with multiple specified threads
sam = SAMFile("/tmp/test.bam", 2);
readrange = sam.allRecords;
assert(readrange.empty == false);
read = readrange.front();
assert(read.sequence=="GCTAGCTCAG");
assert(sam.allRecords.array.length == 1);

// testing with no additional threads
sam = SAMFile("/tmp/test.bam", 0);
readrange = sam.allRecords;
assert(readrange.empty == false);
read = readrange.front();
assert(read.sequence=="GCTAGCTCAG");
assert(sam.allRecords.array.length == 1);

// testing SAMReader targets/tid functions
assert(sam.header.nTargets == 1);
assert(sam.header.targetId("Sheila") == 0);
assert(sam.header.targetLength(0) == 20);
assert(sam.header.targetLengths == [20]);
assert(sam.header.targetNames == ["Sheila"]);

1 import std.stdio;
2 import dhtslib.sam;
3 import dhtslib.sam.md : MDItr;
4 import std.algorithm : map;
5 import std.array : array;
6 import std.path : buildPath,dirName;
7 import std.range : drop;
8 hts_set_log_level(htsLogLevel.HTS_LOG_WARNING);
9 hts_log_info(__FUNCTION__, "Testing SAMFile query");
10 hts_log_info(__FUNCTION__, "Loading test file");
11 
12 auto bam = SAMFile(buildPath(dirName(dirName(dirName(dirName(__FILE__)))),"htslib","test","range.bam"), 0);
13 assert(bam.allRecords.array.length == 112);
14 // assert(bam["CHROMOSOME_I"].array.length == 18);
15 // assert(bam["CHROMOSOME_II"].array.length == 34);
16 // assert(bam["CHROMOSOME_III"].array.length == 41);
17 // assert(bam["CHROMOSOME_IV"].array.length == 19);
18 // assert(bam["CHROMOSOME_V"].array.length == 0);
19 assert(bam.query("CHROMOSOME_I", ZBHO(900, 2000)) .array.length == 14);
20 assert(bam["CHROMOSOME_I",ZB(900) .. ZB(2000)].array.length == 14);
21 assert(bam[0, ZB(900) .. ZB(2000)].array.length == 14);
22 
23 assert(bam["CHROMOSOME_I",ZB(940)].array.length == 2);
24 assert(bam[0, ZB(940)].array.length == 2);
25 
26 
27 assert(bam["CHROMOSOME_I",ZB(900) .. $].array.length == 18);
28 assert(bam[0, ZB(900) .. $].array.length == 18);
29 assert(bam["CHROMOSOME_I",$].array.length == 0);
30 assert(bam[0, $].array.length == 0);
31 assert(bam[["CHROMOSOME_I:900-2000","CHROMOSOME_II:900-2000"]].array.length == 33);
32 
33 assert(bam.query("CHROMOSOME_I", OBHO(901, 2000)) .array.length == 14);
34 assert(bam["CHROMOSOME_I",OB(901) .. OB(2001)].array.length == 14);
35 assert(bam[0, OB(901) .. OB(2001)].array.length == 14);
36 
37 assert(bam["CHROMOSOME_I",OB(941)].array.length == 2);
38 assert(bam[0, OB(941)].array.length == 2);
39 
40 
41 assert(bam["CHROMOSOME_I",OB(901) .. $].array.length == 18);
42 assert(bam[0, OB(901) .. $].array.length == 18);
43 assert(bam["CHROMOSOME_I",$].array.length == 0);
44 assert(bam[0, $].array.length == 0);
45 assert(bam[["CHROMOSOME_I:900-2000","CHROMOSOME_II:900-2000"]].array.length == 33);
46 
47 assert(bam["CHROMOSOME_II",$-1918 .. $].array.length == 0);
48 assert(bam["CHROMOSOME_II", ZB(3082) .. $].array.length == 0);
49 assert(bam["CHROMOSOME_II",$-1919 .. $].array.length == 1);
50 assert(bam["CHROMOSOME_II", ZB(3081) .. $].array.length == 1);
51 assert(bam["CHROMOSOME_II",$-2018 .. $].array.length == 2);
52 
53 auto range = bam[["CHROMOSOME_I:900-2000","CHROMOSOME_II:900-2000"]];
54 auto range1 = range.save;
55 range = range.drop(5);
56 auto range2 = range.save;
57 range = range.drop(5);
58 auto range3 = range.save;
59 range = range.drop(10);
60 auto range4 = range.save;
61 assert(range1.array.length == 33);
62 assert(range2.array.length == 28);
63 assert(range3.array.length == 23);
64 assert(range4.array.length == 13);

import std.stdio;
import dhtslib.sam;
import std.array : array;
import std.path : buildPath,dirName;
import std.range : drop;
hts_set_log_level(htsLogLevel.HTS_LOG_WARNING);
hts_log_info(__FUNCTION__, "Testing RecordsRange save()");
hts_log_info(__FUNCTION__, "Loading test file");

auto bam = SAMReader(buildPath(dirName(dirName(dirName(dirName(__FILE__)))),"htslib","test","range.bam"), 4);

auto range = bam.query("CHROMOSOME_I", ZBHO(900, 2000));
assert(bam.query("CHROMOSOME_I", ZBHO(900, 2000)).array.length == 14);

auto range1 =  range.save;
range = range.drop(1);

auto range2 =  range.save;
range = range.drop(2);

auto range3 =  range.save;
range = range.drop(3);

auto range4 =  range.save;
range = range.drop(5);

auto range5 =  range.save;
range.popFront;

auto range6 = range.save;

assert(range1.array.length == 14);
assert(range2.array.length == 13);
assert(range3.array.length == 11);
assert(range4.array.length == 8);
assert(range5.array.length == 3);
assert(range6.array.length == 2);

SAMReader

Constructors

Members

Aliases

Functions

Properties

Structs

Variables

Examples

Meta

Source