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Use system htslib; a couple minor tweaks #64

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e656a80
Merge branch 'master' of github.com:walaj/SeqLib into jh_nov2018
julianhess Sep 10, 2019
31f629f
Remove internal dependency on htslib
julianhess Sep 10, 2019
4d34d90
Merge branch 'jh_nov2018' into new_hts
julianhess Sep 10, 2019
7a4a68b
Make Num(Hard|Soft)Clipped more efficient
julianhess Sep 25, 2019
e773689
Merge branch 'master' of github.com:walaj/SeqLib
julianhess Mar 26, 2021
9f589fa
Add BamReader::GetRegionIdx
julianhess Mar 26, 2021
db79b50
Remove a couple new htslib build references
julianhess Mar 26, 2021
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4 changes: 2 additions & 2 deletions Makefile.am
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
AUTOMAKE_OPTIONS = foreign
SUBDIRS = bwa htslib fermi-lite src
SUBDIRS = bwa fermi-lite src

install:
mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib
mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a lib

seqtools:
mkdir -p bin && cd src/seqtools && make && mv seqtools ../../bin
4 changes: 2 additions & 2 deletions Makefile.in
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Original file line number Diff line number Diff line change
Expand Up @@ -296,7 +296,7 @@ top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
AUTOMAKE_OPTIONS = foreign
SUBDIRS = bwa htslib fermi-lite src
SUBDIRS = bwa fermi-lite src
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-recursive

Expand Down Expand Up @@ -778,7 +778,7 @@ uninstall-am:


install:
mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib
mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a lib

seqtools:
mkdir -p bin && cd src/seqtools && make && mv seqtools ../../bin
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8 changes: 4 additions & 4 deletions SeqLib/BamHeader.h
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
#ifndef SEQLIB_BAM_HEADER_H__
#define SEQLIB_BAM_HEADER_H__

#include "htslib/htslib/hts.h"
#include "htslib/htslib/sam.h"
#include "htslib/htslib/bgzf.h"
#include "htslib/htslib/kstring.h"
#include <htslib/hts.h>
#include <htslib/sam.h>
#include <htslib/bgzf.h>
#include <htslib/kstring.h>

#include "SeqLib/SeqLibUtils.h"
#include <string>
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5 changes: 5 additions & 0 deletions SeqLib/BamReader.h
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Expand Up @@ -174,6 +174,11 @@ class BamReader {
*/
bool SetMultipleRegions(const GRC& grc);

/** Return the current region index
* @return current region index
*/
size_t GetRegionIdx();

/** Return if the reader has opened the first file */
bool IsOpen() const { if (m_bams.size()) return m_bams.begin()->second.fp.get() != NULL; return false; }

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38 changes: 18 additions & 20 deletions SeqLib/BamRecord.h
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Expand Up @@ -10,11 +10,11 @@
#include <algorithm>

extern "C" {
#include "htslib/htslib/hts.h"
#include "htslib/htslib/sam.h"
#include "htslib/htslib/bgzf.h"
#include "htslib/htslib/kstring.h"
#include "htslib/htslib/faidx.h"
#include <htslib/hts.h>
#include <htslib/sam.h>
#include <htslib/bgzf.h>
#include <htslib/kstring.h>
#include <htslib/faidx.h>

}

Expand Down Expand Up @@ -665,31 +665,29 @@ class BamRecord {
inline int32_t NumSoftClip() const {
int32_t p = 0;
uint32_t* c = bam_get_cigar(b);
for (size_t i = 0; i < b->core.n_cigar; ++i)
if (bam_cigar_opchr(c[i]) == 'S')
p += bam_cigar_oplen(c[i]);

p = (((*c) & 0xF) == BAM_CSOFT_CLIP ? ((*c) >> 4) : 0);
c += b->core.n_cigar - 1;
p += (((*c) & 0xF) == BAM_CSOFT_CLIP ? ((*c) >> 4) : 0);

return p;
}
}

/** Get the number of hard clipped bases */
inline int32_t NumHardClip() const {
int32_t p = 0;
uint32_t* c = bam_get_cigar(b);
for (size_t i = 0; i < b->core.n_cigar; ++i)
if (bam_cigar_opchr(c[i]) == 'H')
p += bam_cigar_oplen(c[i]);
return p;
}

p = (((*c) & 0xF) == BAM_CHARD_CLIP ? ((*c) >> 4) : 0);
c += b->core.n_cigar - 1;
p += (((*c) & 0xF) == BAM_CHARD_CLIP ? ((*c) >> 4) : 0);

return p;
}

/** Get the number of clipped bases (hard clipped and soft clipped) */
inline int32_t NumClip() const {
int32_t p = 0;
uint32_t* c = bam_get_cigar(b);
for (size_t i = 0; i < b->core.n_cigar; ++i)
if ( (bam_cigar_opchr(c[i]) == 'S') || (bam_cigar_opchr(c[i]) == 'H') )
p += bam_cigar_oplen(c[i]);
return p;
return NumSoftClip() + NumHardClip();
}

/** Get a string (Z) tag
Expand Down
2 changes: 1 addition & 1 deletion SeqLib/RefGenome.h
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Expand Up @@ -5,7 +5,7 @@
#include <cstdlib>
#include <iostream>

#include "htslib/htslib/faidx.h"
#include <htslib/faidx.h>

namespace SeqLib {

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2 changes: 1 addition & 1 deletion bwa
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Submodule bwa updated 18 files
+3 −1 Makefile
+49 −0 NEWS.md
+2 −2 bwa.1
+5 −2 bwa.c
+7 −0 bwa.h
+2 −2 bwakit/run-bwamem
+25 −0 bwamem.c
+1 −0 bwamem.h
+3 −1 bwamem_extra.c
+6 −1 bwamem_pair.c
+1 −1 bwape.c
+1 −0 bwase.c
+1 −1 bwtsw2_pair.c
+3 −1 fastmap.c
+1 −1 kstring.h
+10 −16 kthread.c
+1 −1 main.c
+1 −1 qualfa2fq.pl
1 change: 0 additions & 1 deletion htslib
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Submodule htslib deleted from 49fdfb
5 changes: 5 additions & 0 deletions src/BamReader.cpp
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Expand Up @@ -141,6 +141,11 @@ void BamReader::Reset() {
return false;
}

size_t BamReader::GetRegionIdx() {
// this ought to be in sync across all open BAMs
return m_bams.begin()->second.m_region_idx;
}

bool BamReader::Open(const std::string& bam) {

// dont open same bam twice
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2 changes: 1 addition & 1 deletion src/ReadFilter.cpp
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#include "SeqLib/ReadFilter.h"

#include <cassert>
#include "htslib/htslib/khash.h"
#include <htslib/khash.h>

//#define QNAME "D0EN0ACXX111207:7:2306:6903:136511"
//#define QFLAG -1
Expand Down