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Mark duplicates in files with many contigs #361

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merged 2 commits into from
Aug 29, 2018
Merged

Mark duplicates in files with many contigs #361

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bb1ac78
Increase the maximum number of contigs and libraries supported by mar…
dpryan79 Aug 27, 2018
eefaf90
Allow the full number of contigs supported by a BAM file.
dpryan79 Aug 28, 2018
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24 changes: 12 additions & 12 deletions sambamba/markdup.d
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Original file line number Diff line number Diff line change
Expand Up @@ -558,14 +558,14 @@ auto readPairsAndFragments(alias hashFunc=simpleHash, R)
(reads, table_size_log2, overflow_list_size, tmp_dir, task_pool);
}

/////////////////////////////////////////////////////////////////////////////////
/// no more than 32767 libraries and 16383 reference sequences are supported ////
/////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////
/// no more than 536 million libraries and 2 billion reference sequences are supported ////
///////////////////////////////////////////////////////////////////////////////////////////

// 8 bytes
struct SingleEndBasicInfo {
mixin(bitfields!(short, "library_id", 16,
ushort, "ref_id", 14,
mixin(bitfields!(int, "library_id", 30,
uint, "ref_id", 32,
ubyte, "reversed", 1,
ubyte, "paired", 1));
int coord;
Expand All @@ -575,7 +575,7 @@ struct SingleEndBasicInfo {
reversed == other.reversed && library_id == other.library_id;
}
}
static assert(SingleEndBasicInfo.sizeof == 8);
static assert(SingleEndBasicInfo.sizeof == 16);

struct SingleEndInfo {
SingleEndBasicInfo basic_info;
Expand All @@ -585,13 +585,13 @@ struct SingleEndInfo {
}

struct PairedEndsInfo {
mixin(bitfields!(short, "library_id", 16,
ushort, "ref_id1", 14,
mixin(bitfields!(long, "library_id", 30,
uint, "ref_id1", 32,
ubyte, "reversed1", 1,
ubyte, "reversed2", 1));
int coord1;
int coord2;
ushort ref_id2;
uint ref_id2;

uint score; // sum of base qualities that are >= 15
ulong idx1, idx2;
Expand All @@ -601,7 +601,7 @@ struct PairedEndsInfo {
// HACK! HACK! HACK! use the fact that the structures are almost
// the same except the one bit meaning 'paired' instead of 'reversed2'.
auto p = cast(ubyte*)(&result);
p[0 .. 8] = (cast(ubyte*)(&this))[0 .. 8];
p[0 .. 16] = (cast(ubyte*)(&this))[0 .. 16];
result.paired = true;
return result;
}
Expand Down Expand Up @@ -675,7 +675,7 @@ class ReadGroupIndex {
}
++i;
}
enforce(n_libs <= 32767, "More than 32767 libraries are unsupported");
enforce(n_libs <= 536870911, "More than 536870911 libraries are unsupported");
}

/// -1 if read group with such name is not found in the header
Expand Down Expand Up @@ -762,6 +762,7 @@ SingleEndBasicInfo basicInfo(E)(auto ref E e) {
bool samePosition(E1, E2)(auto ref E1 e1, auto ref E2 e2) {
static if (is(E1 == PairedEndsInfo) && is(E2 == PairedEndsInfo)) {
return *cast(ulong*)(&e1) == *cast(ulong*)(&e2) &&
e1.coord1 == e2.coord1 &&
e1.ref_id2 == e2.ref_id2 && e1.coord2 == e2.coord2;
} else {
return basicInfo(e1).samePosition(basicInfo(e2));
Expand Down Expand Up @@ -1232,7 +1233,6 @@ int markdup_main(string[] args) {
// Set up the BAM reader and pass in the thread pool
auto bam = new MultiBamReader(args[1 .. $-1], taskPool);
auto n_refs = bam.reference_sequences.length;
enforce(n_refs < 16384, "More than 16383 reference sequences are unsupported");

auto rg_index = new ReadGroupIndex(bam.header);

Expand Down