git: c5efaea23b87 - main - biology/bbmap: Update to 38.92

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=c5efaea23b875a30e9a7652734d2c992d44f9fbc

commit c5efaea23b875a30e9a7652734d2c992d44f9fbc
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-08-22 13:59:58 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-08-22 13:59:58 +0000

    biology/bbmap: Update to 38.92
    
    Numerous small fixes and enhancements
    
    Reported by:    portscout
---
 biology/bbmap/Makefile  |  8 +++++---
 biology/bbmap/distinfo  |  6 +++---
 biology/bbmap/pkg-plist | 16 ++++++++++++++--
 3 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile
index 9f20eab70e8c..9527ee8f4076 100644
--- a/biology/bbmap/Makefile
+++ b/biology/bbmap/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	bbmap
-DISTVERSION=	38.90
+DISTVERSION=	38.92
 CATEGORIES=	biology java
 MASTER_SITES=	SF/bbmap/
 DISTNAME=	BBMap_${PORTVERSION}
@@ -23,7 +23,7 @@ WRKSRC=		${WRKDIR}/${PORTNAME}
 NO_BUILD=	yes
 NO_ARCH=	yes
 
-LIBEXEC_DIR=    ${PREFIX}/libexec/bbmap
+LIBEXEC_DIR=	${PREFIX}/libexec/bbmap
 
 pre-configure:
 	${REINPLACE_CMD} -e 's|"$$DIR""current/"|${JAVAJARDIR}/bbmap|g' \
@@ -32,13 +32,15 @@ pre-configure:
 		-e 's|"$$DIR""/calcmem.sh"|${LIBEXEC_DIR}/bbmap/calcmem.sh|g' \
 		${WRKSRC}/*.sh
 
+# FIXME: Find out which scripts are meant to be part of the CLI
 do-install:
 	@${MKDIR} ${STAGEDIR}${LIBEXEC_DIR}
 	@${MKDIR} ${STAGEDIR}${JAVAJARDIR}/bbmap
 	${INSTALL_SCRIPT} ${WRKSRC}/*.sh ${STAGEDIR}${LIBEXEC_DIR}
 	cd ${WRKSRC}/current && ${COPYTREE_SHARE} . \
 		${STAGEDIR}${JAVAJARDIR}/bbmap
-.for f in bbduk.sh bbnorm.sh dedupe.sh bbmap.sh bloomfilter.sh reformat.sh
+.for f in bbduk.sh bbnorm.sh dedupe.sh bbmap.sh bloomfilter.sh reformat.sh \
+	bbmerge.sh tadpole.sh
 	${RLN} ${STAGEDIR}${LIBEXEC_DIR}/${f} ${STAGEDIR}${PREFIX}/bin
 .endfor
 
diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo
index 2dcabac6c8b8..391a7c547bee 100644
--- a/biology/bbmap/distinfo
+++ b/biology/bbmap/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1618324169
-SHA256 (BBMap_38.90.tar.gz) = a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1
-SIZE (BBMap_38.90.tar.gz) = 10516866
+TIMESTAMP = 1629639676
+SHA256 (BBMap_38.92.tar.gz) = a5db3921684296dcbcabd0d36dc123597f587a6ac96855f4f901fee494718dc3
+SIZE (BBMap_38.92.tar.gz) = 10669924
diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist
index 195fa6f86ab3..d4d5cbf8b549 100644
--- a/biology/bbmap/pkg-plist
+++ b/biology/bbmap/pkg-plist
@@ -1,9 +1,11 @@
 bin/bbduk.sh
 bin/bbmap.sh
+bin/bbmerge.sh
 bin/bbnorm.sh
 bin/bloomfilter.sh
 bin/dedupe.sh
 bin/reformat.sh
+bin/tadpole.sh
 libexec/bbmap/a_sample_mt.sh
 libexec/bbmap/addadapters.sh
 libexec/bbmap/addssu.sh
@@ -1184,6 +1186,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/jgi/Seal$ProcessThread.class
 %%JAVAJARDIR%%/bbmap/jgi/Seal.class
 %%JAVAJARDIR%%/bbmap/jgi/Seal.java
+%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.class
+%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.java
 %%JAVAJARDIR%%/bbmap/jgi/Shred.class
 %%JAVAJARDIR%%/bbmap/jgi/Shred.java
 %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class
@@ -1233,8 +1237,6 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java
 %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class
 %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java
-%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.class
-%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.java
 %%JAVAJARDIR%%/bbmap/kmer/DumpThread.class
 %%JAVAJARDIR%%/bbmap/kmer/DumpThread.java
 %%JAVAJARDIR%%/bbmap/kmer/HashArray.class
@@ -1553,6 +1555,12 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class
 %%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class
 %%JAVAJARDIR%%/bbmap/sort/SortReadsByID.java
+%%JAVAJARDIR%%/bbmap/star/Ship.class
+%%JAVAJARDIR%%/bbmap/star/Ship.java
+%%JAVAJARDIR%%/bbmap/star/Simulate.class
+%%JAVAJARDIR%%/bbmap/star/Simulate.java
+%%JAVAJARDIR%%/bbmap/star/Weapon.class
+%%JAVAJARDIR%%/bbmap/star/Weapon.java
 %%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class
 %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class
 %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java
@@ -1726,6 +1734,10 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.java
 %%JAVAJARDIR%%/bbmap/structures/LongList.class
 %%JAVAJARDIR%%/bbmap/structures/LongList.java
+%%JAVAJARDIR%%/bbmap/structures/LongList2.class
+%%JAVAJARDIR%%/bbmap/structures/LongList2.java
+%%JAVAJARDIR%%/bbmap/structures/LongList3.class
+%%JAVAJARDIR%%/bbmap/structures/LongList3.java
 %%JAVAJARDIR%%/bbmap/structures/LongListSet$LongListSetIterator.class
 %%JAVAJARDIR%%/bbmap/structures/LongListSet.class
 %%JAVAJARDIR%%/bbmap/structures/LongListSet.java