Releasing v0.8.1 with performance details

Author: pjotrp

INSTALL.md

@@ -37,7 +37,17 @@ container with
     env CC=gcc make -f Makefile.guix -j 8
     make -f Makefile.guix check
 
-Note that this also works in the emacs shell.
+To make the static release:
+
+    env CC=gcc make -f Makefile.guix static
+
+It gives some errors, but should work:
+
+    ./bin/sambamba
+
+When you only get unit tests disable them with `--DRT-testmode=run-main`
+
+Note that this all also works in the emacs shell.
 
 ### Guix VM
 

RELEASE-NOTES.md

@@ -1,8 +1,8 @@
-## ChangeLog v0.8.1 (2020??)
+## ChangeLog v0.8.1 (20210731)
 
 + Some FASTA unittests break when they write to disk and read after -
   marked with ~version(Broken)~
-+ Fix build for LDC 1.26.0 and LLVM 9.0.1
++ Fix build for LDC 1.26.0 and LLVM 9.0.1 - some speed improvement
 
 ## ChangeLog v0.8.0 (20201130)
 

VERSION

@@ -1 +1 @@
-0.8.1-pre1
+0.8.1

sambamba/main.d

@@ -83,7 +83,7 @@ For bug reports and feature requests see
 
 void printVersion() {
     stderr.writeln();
-    stderr.writeln("sambamba " ~ VERSION ~ " by Artem Tarasov and Pjotr Prins (C) 2012-2020");
+    stderr.writeln("sambamba " ~ VERSION ~ " by Artem Tarasov and Pjotr Prins (C) 2012-2021");
     stderr.writeln("    LDC " ~ LDC_VERSION_STRING ~ " / DMD " ~ DMD_VERSION_STRING ~
      " / LLVM" ~ LLVM_VERSION_STRING ~ " / bootstrap " ~ BOOTSTRAP_VERSION_STRING);
     stderr.writeln();

test/benchmark/stats.org

@@ -7,6 +7,38 @@ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00100/alignment/HG00
 
 
 ** View
+
+Processing an 841Mb BAM file.
+
+*** AMD Ryzen 7 3700X 8-Core Processor
+
+#+BEGIN_SRC
+time ./bin/sambamba-0.8.1-pre1 HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam > /dev/null
+
+sambamba 0.8.1-pre1
+ by Artem Tarasov and Pjotr Prins (C) 2012-2021
+    LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
+real    0m1.398s
+user    0m16.589s
+sys     0m0.240s
+
+time ./bin/sambamba-0.8.1-pre1 sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
+
+sambamba 0.8.1-pre1
+ by Artem Tarasov and Pjotr Prins (C) 2012-2021
+    LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
+real    0m9.151s
+user    2m5.779s
+sys     0m3.101s
+
+time ./bin/sambamba-0.8.1-pre1 markdup HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.sorted.bam dedup.bam
+ by Artem Tarasov and Pjotr Prins (C) 2012-2021
+    LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
+real    0m11.319s
+user    1m47.719s
+sys     0m4.070s
+#+END_SRC
+
 *** 4x Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz (hyperthreaded)
 **** sambamba 0.6.8-pre3