From 1697e38b976c5a154192df998e444d172f6387b1 Mon Sep 17 00:00:00 2001 From: Guoyi Zhang Date: Sat, 14 Sep 2024 16:51:22 +1000 Subject: [PATCH] fix: some error and typo --- RGBEPP.d | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RGBEPP.d b/RGBEPP.d index c946065..b0eb4a3 100644 --- a/RGBEPP.d +++ b/RGBEPP.d @@ -180,7 +180,7 @@ void processMappingDenovo(string[] ARG_L, int ARG_T, string DirQcTrim, string Di createDir(DirMap); createDir(DirMap ~ "/index"); string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds"; - string DirAssemblyFas = DirAssemblySca ~ "/" ~ "fasta"; + string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta"; createDir(DirAssemblySca); createDir(DirAssemblyFas); string ReferDmnd = DirAssemblySca ~ "/" ~ "Reference.dmnd"; @@ -196,7 +196,7 @@ void processMappingDenovo(string[] ARG_L, int ARG_T, string DirQcTrim, string Di string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz"; string outputBam = DirMap ~ "/" ~ baseName ~ ".bam"; - string[] cmdDiamond = ["diamond", "blastx", "-d", ReferDmnd, "-q", inputFasta, "-o", inputM8, "--outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen gaps ppos qframe qseq"]; + string[] cmdDiamond = ["diamond", "blastx", "-d", "Reference.dmnd", "-q", inputFasta, "-o", inputM8, "--outfmt", "6", "qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore", "qlen", "slen", "gaps", "ppos", "qframe", "qseq"]; string[] cmdSortDiamond = ["sortdiamond", inputM8, outputSort]; string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, outputSort, outputIndex]; string[] cmdMap = [PathBowtie2, "-x", outputIndex, "-1", inputFileR1, "-2", inputFileR2, "-p", ARG_T.to!string];