From 1e46798bfb3dff428c0cb6fcd00c0d5299b302bf Mon Sep 17 00:00:00 2001 From: Haoyu Cheng Date: Thu, 2 Jan 2020 08:58:50 +0800 Subject: [PATCH] update readme and help information --- CommandLines.cpp | 3 ++- README.md | 7 ++----- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/CommandLines.cpp b/CommandLines.cpp index 8114b45..88593d9 100644 --- a/CommandLines.cpp +++ b/CommandLines.cpp @@ -28,7 +28,8 @@ void Print_H(hifiasm_opt_t* asm_opt) fprintf(stderr, " -k INT k-mer length [%d] (must be < 64)\n", asm_opt->k_mer_length); ///fprintf(stderr, " -w write all overlaps to disk, can accelerate assembly next time [%d]\n", asm_opt->write_index_to_disk); ///fprintf(stderr, " -l load all overlaps from disk, can avoid overlap calculation [%d]\n", asm_opt->load_index_from_disk); - fprintf(stderr, " -i ignore saved overlaps in *.ovlp*.bin files\n"); + ///fprintf(stderr, " -i ignore saved overlaps in *.ovlp*.bin files\n"); + fprintf(stderr, " -i ignore saved overlaps in *.ovlp* files\n"); fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen); fprintf(stderr, " -p INT size of popped bubbles [%lld]\n", asm_opt->pop_bubble_size); fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate); diff --git a/README.md b/README.md index 9849247..31ab920 100644 --- a/README.md +++ b/README.md @@ -33,9 +33,7 @@ outputs consist of: So far hifiasm is still in early development stage, it will output phased chromosome-level high-quality assembly in the near future. In addition, hifiasm also outputs three binary files that save all overlap inforamtion -(hifiasm.asm.gfa.aux.bin, hifiasm.asm.gfa.aux.reverse.bin, -hifiasm.asm.gfa.aux.source.bin in default). With these files, hifiasm can avoid -the time-consuming all-to-all overlap calculation step, and do the assembly +(hifiasm.asm.ovlp, hifiasm.asm.ovlp.source, hifiasm.asm.ovlp.reverse in default). With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step, and do the assembly directly and quickly. This might be helpful when you want to get an optimized assembly by multiple round of experiments with different parameters. @@ -70,8 +68,7 @@ all overlaps to disk, which can avoid the time-consuming all-to-all overlap calculation next time. For hifiasm, once the overlap information has been obtained during the previous run in advance, it is able to load all overlaps from disk and then directly do assembly. If you want to ignore the pre-computed -overlap information, please specify `-i` or simply delete `*gfa.aux.bin`, -`*gfa.aux.reverse.bin` and `*gfa.aux.source.bin`. +overlap information, please specify `-i` or simply delete `*.ovlp`, `*.ovlp.source` and `*.ovlp.reverse`. Please note that some old Hifi reads may consist of short adapters. To improve the assembly quality, adapters should be removed by `-z` as follow: