Merge branch 'release/5.4.0'

CHANGES.md

@@ -1,5 +1,11 @@
 # CHANGES
 
+## 5.4.0
+
+* Update base image of docker to cgpbigwig 1.5.0
+* Update to htslib 1.11
+* Update to samtools 1.11 - to handle long running markdup issue
+
 ## 5.3.0
 
 * Support for paired FASTQ names ending with `_R1_001` and `_R2_001` in addition to `_1` and `_2` as before.

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/wtsicgp/cgpbigwig:1.3.0 as builder
+FROM quay.io/wtsicgp/cgpbigwig:1.5.0 as builder
 
 USER  root
 
@@ -11,8 +11,8 @@ ARG BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2
 ARG STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz"
 ARG VER_BIODBHTS="3.01"
 ARG VER_BWA="v0.7.17"
-ARG VER_HTSLIB="1.10.2"
-ARG VER_SAMTOOLS="1.10"
+ARG VER_HTSLIB="1.11"
+ARG VER_SAMTOOLS="1.11"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends apt-transport-https
@@ -62,7 +62,7 @@ FROM  ubuntu:20.04
 
 LABEL maintainer="cgphelp@sanger.ac.uk"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="5.3.0" \
+      version="5.4.0" \
       description="pcap-core"
 
 ENV OPT /opt/wtsi-cgp

c/c_tests/02_bam_access_tests.c

@@ -21,37 +21,6 @@
 #include "minunit.h"
 #include "bam_access.h"
 
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
-    size_t l, m;
-    char *s;
-} kstring_t;
-#endif
-
-static inline int kputsn(const char *p, int l, kstring_t *s)
-{
-	if (s->l + l + 1 >= s->m) {
-		s->m = s->l + l + 2;
-		kroundup32(s->m);
-		s->s = (char*)realloc(s->s, s->m);
-	}
-	memcpy(s->s + s->l, p, l);
-	s->l += l;
-	s->s[s->l] = 0;
-	return l;
-}
-
-
-static inline int kputs(const char *p, kstring_t *s)
-{
-	return kputsn(p, strlen(p), s);
-}
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
 char *test_bam = "../t/data/Stats.bam";
 char *exp_plat = "GAII";
 char *exp_sample = "PD1234a";

lib/PCAP.pm

@@ -28,7 +28,7 @@ use FindBin qw($Bin);
 use File::Which qw(which);
 # don't use autodie, only core perl in here
 
-our $VERSION = '5.3.0';
+our $VERSION = '5.4.0';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

setup.sh

@@ -9,8 +9,8 @@ export BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0p
 export STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz"
 export VER_BIODBHTS="3.01"
 export VER_BWA="v0.7.17"
-export VER_HTSLIB="1.10.2"
-export VER_SAMTOOLS="1.10"
+export VER_HTSLIB="1.11"
+export VER_SAMTOOLS="1.11"
 
 
 if [[ ($# -ne 1 && $# -ne 2) ]] ; then