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Made compile with removed alias this in Nullable #480

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Sep 14, 2021
Merged

Made compile with removed alias this in Nullable #480

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63 changes: 33 additions & 30 deletions BioD/bio/std/experimental/hts/bam/reader.d
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ import std.string;
import std.typecons;
import std.bitmanip;

//TODO remove these dependecies
//TODO remove these dependecies
import bio.std.hts.bam.cigar;
import bio.std.hts.bam.constants;

Expand Down Expand Up @@ -234,28 +234,28 @@ struct ProcessReadBlob {
}

@property void cleanup() {
_read2.cleanup;
_read2.get.cleanup;
}

@property nothrow bool isNull() {
return _read2.isNull;
}

@property RefId ref_id() {
enforce(_read2.is_mapped,"Trying to get ref_id an unmapped read " ~ to!string(_read2));
return _read2.refid;
enforce(_read2.get.is_mapped,"Trying to get ref_id an unmapped read " ~ to!string(_read2));
return _read2.get.refid;
}

@property RefId raw_ref_id() {
return _read2.refid;
return _read2.get.refid;
}

@property nothrow uint _flag_nc() {
return _read2._flag_nc;
return _read2.get._flag_nc;
}

@property nothrow ushort _flag() {
return _read2._flag;
return _read2.get._flag;
}

alias ref_id refid;
Expand All @@ -264,24 +264,24 @@ struct ProcessReadBlob {
/// start_loc), i.e., the first base that gets consumed in the
/// CIGAR.
@property GenomePos start_pos() {
assert(_read2.is_mapped,"Trying to get pos on an unmapped read"); // BAM spec
asserte(_read2.pos < GenomePos.max);
return cast(GenomePos)_read2.pos;
assert(_read2.get.is_mapped,"Trying to get pos on an unmapped read"); // BAM spec
asserte(_read2.get.pos < GenomePos.max);
return cast(GenomePos)_read2.get.pos;
}

@property GenomePos raw_start_pos() {
return cast(GenomePos)_read2.pos;
return cast(GenomePos)_read2.get.pos;
}

/// Get the end position on the reference sequence (better use end_loc)
@property GenomePos end_pos() {
assert(sequence_length > 0, "Trying to get end_pos on an empty read sequence");
assert(!consumed_reference_bases.isNull);
return start_pos + consumed_reference_bases;
return start_pos + consumed_reference_bases.get;
}

@property GenomePos raw_end_pos() {
return raw_start_pos + consumed_reference_bases;
return raw_start_pos + consumed_reference_bases.get;
}

@property GenomeLocation start_loc() {
Expand All @@ -293,27 +293,27 @@ struct ProcessReadBlob {
}

@property @trusted MappingQuality mapping_quality() { // MAPQ
assert(_read2.is_mapped,"Trying to get MAPQ on an unmapped read"); // BAM spec
return MappingQuality(_read2.mapping_quality);
assert(_read2.get.is_mapped,"Trying to get MAPQ on an unmapped read"); // BAM spec
return MappingQuality(_read2.get.mapping_quality);
}

@property @trusted int tlen() { // do not use
return _read2._tlen;
return _read2.get._tlen;
}

@property @trusted GenomePos sequence_length() {
if (sequence_length2.isNull)
sequence_length2 = _read2.sequence_length;
return sequence_length2;
sequence_length2 = _read2.get.sequence_length;
return sequence_length2.get;
}

/// Count and caches consumed reference bases. Uses raw_cigar to
/// avoid a heap allocation.
@property @trusted Nullable!GenomePos consumed_reference_bases() {
if (consumed_reference_bases2.isNull) {
assert(_read2.is_mapped,"Trying to get consumed bases on an unmapped read"); // BAM spec
assert(_read2.get.is_mapped,"Trying to get consumed bases on an unmapped read"); // BAM spec
assert(!read_name.isNull,"Trying to get CIGAR on RNAME is '*'"); // BAM spec
auto raw = cast(uint[]) _read2.raw_cigar();
auto raw = cast(uint[]) _read2.get.raw_cigar();
if (raw.length==1 && raw[0] == '*')
return consumed_reference_bases2; // null
else {
Expand All @@ -332,11 +332,14 @@ struct ProcessReadBlob {
/// Count query consumed bases. Uses raw_cigar to avoid a heap
/// allocation.
@property @trusted GenomePos consumed_query_bases() {
assert(_read2.is_mapped,"Trying to get consumed bases on an unmapped read"); // BAM spec
assert(_read2.get.is_mapped,"Trying to get consumed bases on an unmapped read"); // BAM spec
assert(!read_name.isNull,"Trying to get CIGAR on RNAME is '*'"); // BAM spec
auto raw = cast(uint[]) _read2.raw_cigar();
auto raw = cast(uint[]) _read2.get.raw_cigar();
if (raw.length==1 && raw[0] == '*')
return consumed_reference_bases2; // null
// The existing comment here says "null", but function return type
// forces reading the value anyway. Bug?
// -Nix packager
return consumed_reference_bases2.get; // null
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I also spotted a potential bug while doing this and left a comment accordingly

else {
GenomePos bases = 0;
for (size_t i = 0; i < raw.length; i++) {
Expand All @@ -352,8 +355,8 @@ struct ProcessReadBlob {
/// null. Caches name.
@property Nullable!string read_name() {
if (read_name2.isNull) {
assert(_read2.is_mapped,"Trying to get RNAME on an unmapped read"); // BAM spec
auto raw = _read2.read_name;
assert(_read2.get.is_mapped,"Trying to get RNAME on an unmapped read"); // BAM spec
auto raw = _read2.get.read_name;
if (raw.length == 0 || (raw.length ==1 && raw[0] == '*'))
return read_name2; // null
assert(raw.length < 255); // BAM spec
Expand All @@ -368,9 +371,9 @@ struct ProcessReadBlob {
/// operations. Caches Cigar when there are operations.
@property Nullable!CigarOperations cigar() {
if (cigar2.isNull) {
assert(_read2.is_mapped,"Trying to get CIGAR on an unmapped read"); // BAM spec
assert(_read2.get.is_mapped,"Trying to get CIGAR on an unmapped read"); // BAM spec
assert(!read_name.isNull,"Trying to get CIGAR on RNAME is '*'"); // BAM spec
auto raw = cast(uint[]) _read2.raw_cigar();
auto raw = cast(uint[]) _read2.get.raw_cigar();
if (raw.length==0 || (raw.length==1 && raw[0] == '*'))
return cigar2; // null
else {
Expand All @@ -389,7 +392,7 @@ struct ProcessReadBlob {
/// undefined. Caches sequence.
@property Nullable!string sequence() {
if (sequence2.isNull) { // is it cached in sequence2?
auto raw = _read2.raw_sequence();
auto raw = _read2.get.raw_sequence();
if (raw[0] == '*') {
assert(raw.length == 1);
return sequence2; // null
Expand All @@ -409,7 +412,7 @@ struct ProcessReadBlob {
}

@property ubyte[] toBlob() {
return _read2._data;
return _read2.get._data;
}

@property string posString() {
Expand Down Expand Up @@ -488,7 +491,7 @@ struct BamReadBlobStream {
// void *p = pureMalloc(block_size-2*int.sizeof); // test for GC effectiveness
data = new ubyte[block_size-2*int.sizeof];
readbuf = ReadBlob(refid,pos,stream.read(data));
assert(readbuf._data.ptr == data.ptr);
assert(readbuf.get._data.ptr == data.ptr);
}

}
Expand Down
14 changes: 7 additions & 7 deletions BioD/bio/std/experimental/hts/bgzf.d
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Expand Up @@ -199,7 +199,7 @@ struct BgzfReader {
try {
if (fpos.isNull) throwBgzfException("Trying to read past eof");
report_fpos = fpos;
f.seek(fpos);
f.seek(fpos.get);
immutable compressed_size = read_block_header();
auto ret = read_compressed_data(buffer[0..compressed_size]);
auto compressed_buf = ret[0];
Expand All @@ -209,7 +209,7 @@ struct BgzfReader {
if (uncompressed_size == 0) {
// check for eof marker, rereading block header
auto lastpos = f.tell();
f.seek(start_offset);
f.seek(start_offset.get);
ubyte[BGZF_EOF.length] buf;
f.rawRead(buf);
f.seek(lastpos);
Expand Down Expand Up @@ -412,17 +412,17 @@ struct BgzfStream {
size_t remaining = buffer_length;

while (remaining > 0) {
if (block_pos + remaining < uncompressed_size) {
if (block_pos.get + remaining < uncompressed_size) {
// full copy
assert(buffer_pos + remaining == buffer_length);
memcpy(buffer[buffer_pos..buffer_pos+remaining].ptr,uncompressed_buf[block_pos..block_pos+remaining].ptr,remaining);
block_pos += remaining;
memcpy(buffer[buffer_pos..buffer_pos+remaining].ptr,uncompressed_buf[block_pos.get..block_pos.get+remaining].ptr,remaining);
block_pos.get += remaining;
remaining = 0;
}
else {
// read tail of buffer
immutable tail = uncompressed_size - block_pos;
memcpy(buffer[buffer_pos..buffer_pos+tail].ptr,uncompressed_buf[block_pos..uncompressed_size].ptr,tail);
immutable tail = uncompressed_size - block_pos.get;
memcpy(buffer[buffer_pos..buffer_pos+tail].ptr,uncompressed_buf[block_pos.get..uncompressed_size].ptr,tail);
buffer_pos += tail;
remaining -= tail;
auto res = blockread.read_block(bgzf,fpos,uncompressed_buf);
Expand Down
8 changes: 4 additions & 4 deletions BioD/bio/std/experimental/hts/pileup.d
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Expand Up @@ -271,14 +271,14 @@ class PileUp(R) {
}
ref R read_current() {
enforce(!current.isNull, "current should be set for PileUp.read_current");
return read(current);
return read(current.get);
}
bool is_at_end(RingBufferIndex idx) { return ring.is_tail(idx); }

@property void current_inc() {
asserte(!empty);
asserte(!ring.is_tail(current));
++current;
asserte(!ring.is_tail(current.get));
++current.get;
}

@property void set_current_to_head() {
Expand All @@ -290,7 +290,7 @@ class PileUp(R) {
}

@property bool current_is_tail() {
return ring.is_tail(current);
return ring.is_tail(current.get);
}

void each(void delegate(R) dg) {
Expand Down
10 changes: 5 additions & 5 deletions sambamba/markdup.d
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Expand Up @@ -504,16 +504,16 @@ struct CollateReadPairRange(R, bool keepFragments, alias charsHashFunc)
void popFrontTempFiles() {
while (!_tmp_reads.empty) {
auto r2 = next(_tmp_reads);
if (readsArePaired(_tmp_r1, r2)) {
_front = FrontType(_tmp_r1, r2);
if (readsArePaired(_tmp_r1.get, r2)) {
_front = FrontType(_tmp_r1.get, r2);
if (!_tmp_reads.empty)
_tmp_r1 = next(_tmp_reads);
else
_tmp_r1.nullify();
return;
} else {
static if (keepFragments) {
_front = FrontType(_tmp_r1);
_front = FrontType(_tmp_r1.get);
_tmp_r1 = r2;
return;
} else {
Expand All @@ -523,7 +523,7 @@ struct CollateReadPairRange(R, bool keepFragments, alias charsHashFunc)
}

if (!_tmp_r1.isNull) {
_front = FrontType(_tmp_r1);
_front = FrontType(_tmp_r1.get);
_tmp_r1.nullify();
return;
}
Expand Down Expand Up @@ -1050,7 +1050,7 @@ auto getDuplicateOffsets(R)(R reads, ReadGroupIndex rg_index,
cfg.tmpdir, pool)) {
auto end1 = collectSingleEndInfo(pf.read1, rg_index);
if (!pf.read2.isNull) {
auto end2 = collectSingleEndInfo(pf.read2, rg_index);
auto end2 = collectSingleEndInfo(pf.read2.get, rg_index);
auto pair = combine(end1, end2);
paired_ends.put(pair);
second_ends.put(end2.basic_info);
Expand Down
26 changes: 13 additions & 13 deletions sambamba/pileup.d
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Expand Up @@ -429,28 +429,28 @@ class ChunkDispatcher(ChunkRange) {
}

if (num_ > 1) {
ulong diff = chunk[0].end_position - chunk[0].start_position;
int ref_id = chunk[0].ref_id;
if (ref_id == prev_ref_id && !chunk[0].front.reads.empty &&
prev_pos_diff + diff < chunk[0].front.reads[0].sequence_length) // assume reads are ~same length
ulong diff = chunk.get[0].end_position - chunk.get[0].start_position;
int ref_id = chunk.get[0].ref_id;
if (ref_id == prev_ref_id && !chunk.get[0].front.reads.empty &&
prev_pos_diff + diff < chunk.get[0].front.reads[0].sequence_length) // assume reads are ~same length
stderr.writeln("[WARNING] COVERAGE IS TOO HIGH, INCREASE --buffer-size TO AVOID WRONG RESULTS");
prev_pos_diff = diff;
prev_ref_id = ref_id;
}

auto ref_name = bam_.reference_sequences[chunk[0].ref_id].name;
auto ref_name = bam_.reference_sequences[chunk.get[0].ref_id].name;
auto f = std.stdio.File(filename ~ ".bed", "w");
if (bed_filename is null) {
auto start = chunk[0].start_position;
auto end = chunk[0].end_position;
auto start = chunk.get[0].start_position;
auto end = chunk.get[0].end_position;

auto bed = BedRecord(ref_name, start, end);
f.writeln(bed);
} else {
foreach (reg; regions) {
if (chunk[0].ref_id != reg.ref_id) continue;
auto start = max(reg.start, chunk[0].start_position);
auto end = min(reg.end, chunk[0].end_position);
if (chunk.get[0].ref_id != reg.ref_id) continue;
auto start = max(reg.start, chunk.get[0].start_position);
auto end = min(reg.end, chunk.get[0].end_position);
if (start > end) continue;
auto bed = BedRecord(ref_name, start, end);
f.writeln(bed);
Expand Down Expand Up @@ -525,9 +525,9 @@ void worker(Dispatcher)(Dispatcher d,
if (result.isNull)
return;

auto chunk = result[0];
auto filename = result[1];
auto num = result[2];
auto chunk = result.get[0];
auto filename = result.get[1];
auto num = result.get[2];
makeFifo(filename);

import core.sys.posix.signal;
Expand Down
6 changes: 3 additions & 3 deletions sambamba/subsample.d
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Expand Up @@ -243,7 +243,7 @@ void foreach_invalid_read(ref BamBlobReader reader, void delegate(ProcessReadBlo

// ---- When current is unmapped, move through reads that are ignored.
void foreach_outside_read(ref BamBlobReader reader, void delegate(ProcessReadBlob) dg) {
if (reader.peek.is_unmapped) {
if (reader.peek.get.is_unmapped) {
foreach_invalid_read(reader,dg);
}
}
Expand Down Expand Up @@ -384,13 +384,13 @@ int subsample_main(string[] args) {
}
if (!pileup.empty) {
auto read = reader.peek;
if (read.is_mapped && depth.ref_id != read.refid) {
if (read.get.is_mapped && depth.ref_id != read.get.refid) {
// moving into a new pileup
pileup.purge( (ReadState read) {
write(",");
writer.push(read.read);
});
depth.reset(read.refid);
depth.reset(read.get.refid);
}
}

Expand Down