From 3d96af9eaf60599ee05cd3ffcae1b6622351724c Mon Sep 17 00:00:00 2001 From: Frederic Lemoine Date: Mon, 6 Nov 2023 14:58:10 +0100 Subject: [PATCH] Updated doc for goalign concat -l --- docs/commands/concat.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/commands/concat.md b/docs/commands/concat.md index 6fd36f1..ab06d38 100644 --- a/docs/commands/concat.md +++ b/docs/commands/concat.md @@ -5,6 +5,8 @@ ### concat This command concatenates several alignments in one global alignment. Input alignments may be in phylip or fasta format. If input format is phylip, the file may contain several alignments to concatenate : `goalign concat -i several.phy`. If format is Fasta, all fasta files must be given independently with `goalign concat -i first.fa [second.fa, third.fa, ...]` or `goalign -i none [first.fa, second.Fa, third.fa, ...]`. The order of sequences in alignments may be different, `concat` command will match sequences based on their name. +If `-l` is given, the coordinates of all the input alignments in the concatenated alignment are written in the log file (tab separated values : start (0-based inclusive), end (0-based exclusive), input file name). + #### Usage ``` Usage: @@ -12,7 +14,8 @@ Usage: Flags: -o, --output string Alignment output file (default "stdout") - + -l, --log string Log output file (coordinates of all input alignments + in the concatenated alignment) (default "none") Global Flags: -i, --align string Alignment input file (default "stdin") -p, --phylip Alignment is in phylip? False=Fasta