malacology/RGBEPP
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fix: some error and typo

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This commit is contained in:
kuoi 2024-09-14 16:51:22 +10:00
parent c5928b62f0
commit 1697e38b97
1 changed files with 2 additions and 2 deletions
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4
RGBEPP.d
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@ -180,7 +180,7 @@ void processMappingDenovo(string[] ARG_L, int ARG_T, string DirQcTrim, string Di
createDir(DirMap); createDir(DirMap);
createDir(DirMap ~ "/index"); createDir(DirMap ~ "/index");
string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds"; string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds";
string DirAssemblyFas = DirAssemblySca ~ "/" ~ "fasta"; string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta";
createDir(DirAssemblySca); createDir(DirAssemblySca);
createDir(DirAssemblyFas); createDir(DirAssemblyFas);
string ReferDmnd = DirAssemblySca ~ "/" ~ "Reference.dmnd"; 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 inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
string outputBam = DirMap ~ "/" ~ baseName ~ ".bam"; 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[] cmdSortDiamond = ["sortdiamond", inputM8, outputSort];
string[] cmdBuildDB = [PathBowtie2_build, "--threads", ARG_T.to!string, outputSort, outputIndex]; 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]; string[] cmdMap = [PathBowtie2, "-x", outputIndex, "-1", inputFileR1, "-2", inputFileR2, "-p", ARG_T.to!string];