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lines changed Original file line number Diff line number Diff line change @@ -37,7 +37,17 @@ container with
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env CC=gcc make -f Makefile.guix -j 8
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make -f Makefile.guix check
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- Note that this also works in the emacs shell.
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+ To make the static release:
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+
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+ env CC=gcc make -f Makefile.guix static
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+
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+ It gives some errors, but should work:
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+
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+ ./bin/sambamba
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+
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+ When you only get unit tests disable them with ` --DRT-testmode=run-main `
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+
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+ Note that this all also works in the emacs shell.
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### Guix VM
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Original file line number Diff line number Diff line change 1
- ## ChangeLog v0.8.1 (2020?? )
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+ ## ChangeLog v0.8.1 (20210731 )
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+ Some FASTA unittests break when they write to disk and read after -
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marked with ~ version(Broken)~
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- + Fix build for LDC 1.26.0 and LLVM 9.0.1
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+ + Fix build for LDC 1.26.0 and LLVM 9.0.1 - some speed improvement
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## ChangeLog v0.8.0 (20201130)
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Original file line number Diff line number Diff line change 1
- 0.8.1-pre1
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+ 0.8.1
Original file line number Diff line number Diff line change @@ -83,7 +83,7 @@ For bug reports and feature requests see
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void printVersion () {
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stderr.writeln();
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- stderr.writeln(" sambamba " ~ VERSION ~ " by Artem Tarasov and Pjotr Prins (C) 2012-2020 " );
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+ stderr.writeln(" sambamba " ~ VERSION ~ " by Artem Tarasov and Pjotr Prins (C) 2012-2021 " );
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stderr.writeln(" LDC " ~ LDC_VERSION_STRING ~ " / DMD " ~ DMD_VERSION_STRING ~
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" / LLVM" ~ LLVM_VERSION_STRING ~ " / bootstrap " ~ BOOTSTRAP_VERSION_STRING );
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stderr.writeln();
Original file line number Diff line number Diff line change @@ -7,6 +7,38 @@ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00100/alignment/HG00
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** View
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+
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+ Processing an 841Mb BAM file.
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+
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+ *** AMD Ryzen 7 3700X 8-Core Processor
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+
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+ #+BEGIN_SRC
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+ time ./bin/sambamba-0.8.1-pre1 HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam > /dev/null
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+
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+ sambamba 0.8.1-pre1
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+ by Artem Tarasov and Pjotr Prins (C) 2012-2021
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+ LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
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+ real 0m1.398s
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+ user 0m16.589s
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+ sys 0m0.240s
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+
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+ time ./bin/sambamba-0.8.1-pre1 sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
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+
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+ sambamba 0.8.1-pre1
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+ by Artem Tarasov and Pjotr Prins (C) 2012-2021
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+ LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
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+ real 0m9.151s
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+ user 2m5.779s
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+ sys 0m3.101s
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+
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+ time ./bin/sambamba-0.8.1-pre1 markdup HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.sorted.bam dedup.bam
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+ by Artem Tarasov and Pjotr Prins (C) 2012-2021
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+ LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)
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+ real 0m11.319s
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+ user 1m47.719s
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+ sys 0m4.070s
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+ #+END_SRC
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+
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*** 4x Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz (hyperthreaded)
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**** sambamba 0.6.8-pre3
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