npm i @gmod/bgzf-filehandle Repository github.com/gmod/bgzf-filehandle Homepage github.com/gmod/bgzf-filehandle#readme Weekly Downloads 3,422 Version 2.0.4 License MIT Unpacked Size 65.6 kB Total Files 50 Issues 5 Pull Requests 2 Last publish 3 months ago Collaborators Try on RunKit Report ...
Once indexed, one can extract arbitrary lines from the file with the grab command. Or choose random lines with the, well, random command. There's a ton of room for improvement, but I needed something quickly in support of a side project. Here's a brief example using the simrep.chr1....
4gpus, 48cpus, 192 GB RAM Please specify the steps taken to generate the issue, the command you are running and the relevant output. I am trying to break down a huge bam file so that each file has 50M lines and then run bwakit on the split files as below 130GB fastq file broken ...
Blocked Multi-threaded File Compression UtilityThis utility uses a multithreaded blocked compression algorithm to compress files according the the BAM BGZF format. The files are also compatible with gzip and tabix. This program can be used to reduce run time of most programs that produce BAM files...
针对您遇到的错误信息 [E::sam_index_build3] sam file "nbt.align_filter.bam" not bgzf compressed sam,我们可以从以下几个方面进行分析和解决: 1. 确认错误信息的含义 错误信息表明 nbt.align_filter.bam 文件没有被 BGZF(Block-Gzip Format)压缩,而这是 BAM 文件所必需的。BAM 文件是 SAM 文件的二进制...
BGZF *bgzf_hopen(hFILE *hfp, const char *mode) { BGZF *fp = NULL; assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); if (strchr(mode, 'r')) { fp = bgzf_read_init(hfp); if (fp == NULL) return NULL; } else if (strchr(mode, 'w') || strchr(mode,...
void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading } BGZF; #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifdef __cplusplus extern "C" { #endif /*...
Compress file with bgzipUlrich Wittelsbuerger
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