From 02a333a9b7632b96eb09e28192aed11d8c7db6f6 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Fri, 16 Nov 2018 09:17:57 -0500 Subject: [PATCH] updated for version 0.3 updates --- README.md | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 8ece724..e34d2c2 100644 --- a/README.md +++ b/README.md @@ -26,10 +26,11 @@ This will compile the program using g++, and I'll let you handle where to put it make test ./fastq-scan -h Usage: cat FASTQ | fastq-scan [options] -Version: 0.2 +Version: 0.3 Optional arguments: -g INT Genome size for calculating estimated sequencing coverage. (Default 1) + -p INT ASCII offset for input quality scores, can be 33 or 64. (Default 33) -v Print version information and exit -h Show this message and exit @@ -88,28 +89,32 @@ cat example.fq | ./fastq-scan -g 150000 ### Usage ``` ./fastq-scan -Usage: cat FASTQ | fastq-scan [options] -Version: 0.2 +Usage: cat FASTQ | fastq-scan [options] +Version: 0.3 Optional arguments: -g INT Genome size for calculating estimated sequencing coverage. (Default 1) + -p INT ASCII offset for input quality scores, can be 33 or 64. (Default 33) -v Print version information and exit -h Show this message and exit ``` #### *-g* Genome Size -This is an optional parameter that you can use to estimate the sequencing coverage as calulated by (TOTAL_BP / GENOME_SIZE). By default, the genome size is set to 1. +This is an optional parameter that you can use to estimate the sequencing coverage as calulated by (TOTAL_BP / GENOME_SIZE). By default, the genome size is set to 1. If a genome size is not given the total coverage will not be calculated and instead be set to `0.00` in the final JSON output. + +#### *-p* ASCII Offset for Quality Scores +This optional parameter can be used to explicitely state the ASCII offset for the input quality scores. It defaults to PHRED+33 scores. Only `33` or `64` are valid inputs for this parameter. #### *-v* Version ``` ./fastq-scan -v -fastq-scan 0.2 +fastq-scan 0.3 ``` ### *example.fq* -An example FASTQ file, aptly named *example.fq*, has been included to demonstrate usage of *fastq-scan*. For those interested this is a small set of simulated reads from the [*Lotus japonicus* (NC_002694)](https://www.ncbi.nlm.nih.gov/nuccore/NC_002694.1) chloroplast genome. The reads were simulated using [ART (vMountRainier)](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm). +An example FASTQ file, aptly named *example-q33.fq* (also *example-q64.fq*), has been included to demonstrate usage of *fastq-scan*. For those interested this is a small set of simulated reads from the [*Lotus japonicus* (NC_002694)](https://www.ncbi.nlm.nih.gov/nuccore/NC_002694.1) chloroplast genome. The reads were simulated using [ART (vMountRainier)](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm). ``` -head example.fq +head example-q33.fq @NC_002694.1-75 TGTATACAATAAGAATCCATTTATTGACAAATTTCATTCGAAAATTATGAAACATAAATTTTTTTTTATTGGATCAAGAATTCCAATTTTTTAAGTATAA + @@ -124,7 +129,7 @@ AAAAAGTGAAATATTCAGTTAATGAATGCCGAATCTCCGCTCTTATTCTATGAACATTTCATAATCCTATAAATTATCTT ### Execution ``` -cat example.fq | ./fastq-scan -g 150000 +cat example-q33.fq | ./fastq-scan -g 150000 ```