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Fix build by replacing msgpack
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@pjotrp
pjotrp committed Aug 14, 2023
1 parent 3164efa commit 200ec8a
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Showing 12 changed files with 157 additions and 5,227 deletions.
2 changes: 1 addition & 1 deletion BioD/bio/std/hts/bam/cigar.d
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ import bio.std.hts.utils.array;
import bio.std.hts.utils.value;
import bio.core.utils.switchendianness;

import bio.std.hts.thirdparty.msgpack : Packer, unpack;
import msgpack : Packer, unpack;

/**
Represents single CIGAR operation
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8 changes: 4 additions & 4 deletions BioD/bio/std/hts/bam/read.d
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ import bio.std.hts.utils.array;
import bio.std.hts.utils.value;
import bio.core.utils.switchendianness;

import bio.std.hts.thirdparty.msgpack : Packer, unpack;
import msgpack : Packer, unpack, packer;

import std.algorithm;
import std.range;
Expand Down Expand Up @@ -631,7 +631,7 @@ struct BamRead {

/// Packs message in the following format:
/// $(BR)
/// MsgPack array with elements
/// Msack array with elements
/// $(OL
/// $(LI name - string)
/// $(LI flag - ushort)
Expand Down Expand Up @@ -1353,8 +1353,8 @@ unittest {

{
import std.typecons;
static import bio.std.hts.thirdparty.msgpack;
auto packer = bio.std.hts.thirdparty.msgpack.packer(Appender!(ubyte[])());
// static import msgpack.packer;
auto packer = packer(Appender!(ubyte[])());
read.toMsgpack(packer);
auto data = packer.stream.data;
auto rec = unpack(data).via.array;
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84 changes: 42 additions & 42 deletions BioD/bio/std/hts/bam/tagvalue.d
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,10 @@
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
Expand Down Expand Up @@ -55,16 +55,16 @@ import std.format;
import std.array;
import bio.core.utils.format;

import bio.std.hts.thirdparty.msgpack;
import msgpack;

struct CharToType(char c, T) {
/** symbol */
enum ch = c;

/** type which corresponds to the symbol
according to SAM/BAM specification
according to SAM/BAM specification
*/
alias T ValueType;
alias T ValueType;
}

/**
Expand All @@ -76,22 +76,22 @@ class UnknownTagTypeException : Exception {


alias TypeTuple!(CharToType!('A', char),
CharToType!('c', byte),
CharToType!('c', byte),
CharToType!('C', ubyte),
CharToType!('s', short),
CharToType!('s', short),
CharToType!('S', ushort),
CharToType!('i', int),
CharToType!('i', int),
CharToType!('I', uint),
CharToType!('f', float)) PrimitiveTagValueTypes;

alias TypeTuple!(CharToType!('Z', string),
alias TypeTuple!(CharToType!('Z', string),
CharToType!('H', string)) StringTagValueTypes;

alias TypeTuple!(CharToType!('c', byte),
alias TypeTuple!(CharToType!('c', byte),
CharToType!('C', ubyte),
CharToType!('s', short),
CharToType!('s', short),
CharToType!('S', ushort),
CharToType!('i', int),
CharToType!('i', int),
CharToType!('I', uint),
CharToType!('f', float)) ArrayElementTagValueTypes;

Expand All @@ -112,14 +112,14 @@ uint charToSizeof(char c) {
}
return "switch (c) { " ~ cases.idup ~
" default: " ~
" throw new UnknownTagTypeException(to!string(c));"~
" throw new UnknownTagTypeException(to!string(c));"~
"}";
}
mixin(charToSizeofHelper());
}

/*
Pair of type and its ubyte identifier.
Pair of type and its ubyte identifier.
(Currently, ubyte is enough, but that might change in the future.)
*/
Expand All @@ -131,38 +131,38 @@ struct TypeId(T, ubyte id) {
/*
Structure of type identifier:
0 1
0 1
primitive array/string
something null/nothing numeric string
numeric char 0 0 Z H
integer float 0 [see left 0 0
numeric char 0 0 Z H
integer float 0 [see left 0 0
unsigned signed 0 0 branch] 0 0
[ size in bytes] [size in bytes] 0 [element size] 1 1
(TypeId >> 5) == elementType.sizeof
*/
alias TypeTuple!(TypeId!(char, 0b001_00_1_00),
TypeId!(ubyte, 0b001_0_0000),
TypeId!(ushort, 0b010_0_0000),
TypeId!(uint, 0b100_0__0__0__0__0),
/* Let's take 4 u i n s p
uint as an n n u o r
example b s t m m i

TypeId!(ubyte, 0b001_0_0000),
TypeId!(ushort, 0b010_0_0000),
TypeId!(uint, 0b100_0__0__0__0__0),
/* Let's take 4 u i n s p
uint as an n n u o r
example b s t m m i
y i e e e m
t g g r t i
e n e i h t
s e r c i i
d n v
g e
*/
*/


TypeId!(byte, 0b001_1_0000),
TypeId!(short, 0b010_1_0000),
TypeId!(int, 0b100_1_0000),
TypeId!(short, 0b010_1_0000),
TypeId!(int, 0b100_1_0000),

TypeId!(float, 0b100_01_000),

Expand Down Expand Up @@ -190,7 +190,7 @@ private template GetType(U) {
/// Get tag for type T.
///
/// Useful for comparison with tag field of Value struct.
///
///
/// Example:
/// -----------------------------------
/// Value v = "zzz";
Expand Down Expand Up @@ -251,10 +251,10 @@ string injectOpAssign() {
string injectOpCast() {
char[] cs = "static if".dup;

string injectSwitchPrimitive(string requested_type)
string injectSwitchPrimitive(string requested_type)
{
char[] cs = `switch (_tag) {`.dup;

foreach (t2; PrimitiveTagValueTypes) {
cs ~= `case GetTypeId!`~t2.ValueType.stringof~`: `~
` return to!T(u.`~t2.ch~`);`.dup;
Expand All @@ -266,10 +266,10 @@ string injectOpCast() {
return cs.idup;
}

string injectSwitchArrayElement(string requested_type)
string injectSwitchArrayElement(string requested_type)
{
char[] cs = `switch (_tag) {`.dup;

foreach (t2; ArrayElementTagValueTypes) {
cs ~= `case GetTypeId!(`~t2.ValueType.stringof~`[]): `~
` return to!T(u.B`~t2.ch~`);`.dup;
Expand Down Expand Up @@ -309,10 +309,10 @@ string injectOpCast() {
}

/**
Struct for representing tag values.
Struct for representing tag values.
Tagged union, allows to store
8/16/32-bit integers, floats, chars, strings,
Tagged union, allows to store
8/16/32-bit integers, floats, chars, strings,
and arrays of integers/floats.
*/
struct Value {
Expand All @@ -338,7 +338,7 @@ struct Value {
Currently, type identifier for (u)int requires 8 bits.
Fortunately, SAM/BAM specification doesn't use bigger integer types.
However, in case of need to extend the hierarchy, the type
should be changed from ubyte to something bigger.
should be changed from ubyte to something bigger.
*/
ubyte _tag;

Expand Down Expand Up @@ -382,16 +382,16 @@ struct Value {
this(T)(T value) {
opAssign(value);
}

/// sets 'H' tag instead of default 'Z'. Is not expected to be used much.
void setHexadecimalFlag() {

enforce(this.is_string);

bam_typeid = 'H';
_tag = hexStringTag;

if (_tag != 0b111) {
if (_tag != 0b111) {
u.H = u.Z;
}
}
Expand Down Expand Up @@ -465,7 +465,7 @@ struct Value {
}

/// ditto
void toSam(Sink)(auto ref Sink sink) const
void toSam(Sink)(auto ref Sink sink) const
if (isSomeSink!Sink)
{
if (is_integer) {
Expand Down Expand Up @@ -512,7 +512,7 @@ struct Value {
}

/// ditto
void toJson(Sink)(auto ref Sink sink) const
void toJson(Sink)(auto ref Sink sink) const
if (isSomeSink!Sink)
{
switch (_tag) {
Expand Down
2 changes: 1 addition & 1 deletion BioD/bio/std/hts/sam/header.d
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
*/
module bio.std.hts.sam.header;

import bio.std.hts.thirdparty.msgpack;
import msgpack;
import bio.core.utils.format;

import std.algorithm;
Expand Down
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