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locks; strict;
comment	@# @;


1.3
date	2023.05.17.21.55.34;	author bacon;	state Exp;
branches;
next	1.2;
commitid	27fZ134VGLb3FmpE;

1.2
date	2022.03.17.16.01.11;	author bacon;	state Exp;
branches;
next	1.1;
commitid	Q8UklxdSfTDWnAwD;

1.1
date	2019.01.15.01.26.29;	author bacon;	state Exp;
branches;
next	;
commitid	BDBV5XMtN1wQKO7B;


desc
@@


1.3
log
@biology/hisat2: Add SIMDE support

SIMDE enables SSE and other x86 intrinsics on other architectures
Tested on ARM64, may work on other 64-bit platforms
@
text
@@@comment $NetBSD$
bin/hisat2
bin/hisat2-align-l
bin/hisat2-align-s
bin/hisat2-build
bin/hisat2-build-l
bin/hisat2-build-s
bin/hisat2-inspect
bin/hisat2-inspect-l
bin/hisat2-inspect-s
bin/hisat2-repeat
libexec/hisat2/convert_quals.pl
libexec/hisat2/extract_exons.py
libexec/hisat2/extract_splice_sites.py
libexec/hisat2/gen_2b_occ_lookup.pl
libexec/hisat2/gen_occ_lookup.pl
libexec/hisat2/gen_solqual_lookup.pl
libexec/hisat2/hisat2_extract_exons.py
libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
libexec/hisat2/hisat2_extract_splice_sites.py
libexec/hisat2/hisat2_read_statistics.py
libexec/hisat2/hisat2_simulate_reads.py
libexec/hisat2/infer_fraglen.pl
libexec/hisat2/make_a_thaliana_tair.sh
libexec/hisat2/make_b_taurus_UMD3.sh
libexec/hisat2/make_bdgp6.sh
libexec/hisat2/make_bdgp6_tran.sh
libexec/hisat2/make_canFam2.sh
libexec/hisat2/make_ce10.sh
libexec/hisat2/make_dm6.sh
libexec/hisat2/make_e_coli.sh
libexec/hisat2/make_grch37.sh
libexec/hisat2/make_grch37_snp.sh
libexec/hisat2/make_grch37_snp_tran.sh
libexec/hisat2/make_grch37_snp_tran_ercc.sh
libexec/hisat2/make_grch37_tran.sh
libexec/hisat2/make_grch38.sh
libexec/hisat2/make_grch38_rep.sh
libexec/hisat2/make_grch38_snp.sh
libexec/hisat2/make_grch38_snp_rep.sh
libexec/hisat2/make_grch38_snp_tran.sh
libexec/hisat2/make_grch38_snp_tran_ercc.sh
libexec/hisat2/make_grch38_tran.sh
libexec/hisat2/make_grcm38.sh
libexec/hisat2/make_grcm38_snp.sh
libexec/hisat2/make_grcm38_snp_tran.sh
libexec/hisat2/make_grcm38_tran.sh
libexec/hisat2/make_hg19.sh
libexec/hisat2/make_hg38.sh
libexec/hisat2/make_hg38_allsnp.sh
libexec/hisat2/make_hg38_snp.sh
libexec/hisat2/make_hg38_snp_tran.sh
libexec/hisat2/make_mm10.sh
libexec/hisat2/make_mm9.sh
libexec/hisat2/make_r64.sh
libexec/hisat2/make_r64_tran.sh
libexec/hisat2/make_rn4.sh
libexec/hisat2/make_rn6.sh
libexec/hisat2/make_rnor6.sh
libexec/hisat2/make_rnor6_tran.sh
libexec/hisat2/make_sc3.sh
libexec/hisat2/make_wbcel235.sh
libexec/hisat2/make_wbcel235_tran.sh
libexec/hisat2/make_zm3_snp_tran_ercc.sh
libexec/hisat2/sa.py
libexec/hisat2/validate_repeat.py
@


1.2
log
@biology/hisat2: Update to 2.2.1

pkgsrc fix: Unbreak build on Darwin

Add python3 support
Several bug fixes and enhancements
Changes: https://github.com/DaehwanKimLab/hisat2/tags
@
text
@@


1.1
log
@biology/hisat2: import hisat2-2.1.0.23

HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as to a single reference genome).
@
text
@d11 1
a11 1
libexec/hisat2/compare_HLA_Omixon.py
a12 1
libexec/hisat2/extract_Omixon_HLA.py
d22 1
a23 14
libexec/hisat2/hisatgenotype.py
libexec/hisat2/hisatgenotype_HLA_genotyping_PGs.py
libexec/hisat2/hisatgenotype_assembly_graph.py
libexec/hisat2/hisatgenotype_build_genome.py
libexec/hisat2/hisatgenotype_convert_codis.py
libexec/hisat2/hisatgenotype_extract_codis_data.py
libexec/hisat2/hisatgenotype_extract_cyp_data.py
libexec/hisat2/hisatgenotype_extract_reads.py
libexec/hisat2/hisatgenotype_extract_vars.py
libexec/hisat2/hisatgenotype_gene_typing.py
libexec/hisat2/hisatgenotype_hla_cyp.py
libexec/hisat2/hisatgenotype_locus.py
libexec/hisat2/hisatgenotype_locus_samples.py
libexec/hisat2/hisatgenotype_typing_common.py
d39 1
d41 1
d66 2
a67 5
libexec/hisat2/run_extract_CP.sh
libexec/hisat2/run_extract_ILMN.sh
libexec/hisat2/run_genotype_build.sh
libexec/hisat2/run_hisat2_build.sh
libexec/hisat2/run_type_CP.sh
@