m

.gitignore

@@ -0,0 +1,2 @@
+node_modules
+test

index.js

@@ -98,7 +98,7 @@ const openSam = (filePaths, restraintTo, count) => __awaiter(void 0, void 0, voi
     // await asyncBwaMem('/home/thomas/NGS/ref/ncbi/RNA/human_NM.fa', 
     // ['/Turbine-pool/LAL-T_RNAseq/fastq_fastp/58_MAS/R1.fq.gz','/Turbine-pool/LAL-T_RNAseq/fastq_fastp/58_MAS/R2.fq.gz'],
     // 'TEST', 'TEST', 'test/', console.log)
-    const symbol = 'MYC';
+    const symbol = 'NOTCH1';
     const LRGPath = '/home/thomas/NGS/ref/ncbi/LRG_RefSeqGene';
     const tablePath = '/home/thomas/NGS/ref/ncbi/GCF_000001405.39_GRCh38.p13_feature_table.txt';
     const rnaDBPath = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10].map(n => '/home/thomas/NGS/ref/ncbi/RNA/human.' + n + '.rna.gbff');

index.ts

@@ -85,12 +85,20 @@ const openSam = async (
     return jsonLines
 }
 
+const extractReads = (
+    reads: string[],
+    fastqPaths: string | string[],
+) => {
+    fastqPaths = Array.isArray(fastqPaths) ? fastqPaths : [fastqPaths]
+
+}
+
 (async()=>{
     // await asyncBwaMem('/home/thomas/NGS/ref/ncbi/RNA/human_NM.fa', 
     // ['/Turbine-pool/LAL-T_RNAseq/fastq_fastp/58_MAS/R1.fq.gz','/Turbine-pool/LAL-T_RNAseq/fastq_fastp/58_MAS/R2.fq.gz'],
     // 'TEST', 'TEST', 'test/', console.log)
     
-    const symbol = 'MYC'
+    const symbol = 'NOTCH1'
 
     const LRGPath = '/home/thomas/NGS/ref/ncbi/LRG_RefSeqGene'
     const tablePath = '/home/thomas/NGS/ref/ncbi/GCF_000001405.39_GRCh38.p13_feature_table.txt'