From 891777dc367ea8c6bbebafde80ad4b247a9c4184 Mon Sep 17 00:00:00 2001 From: Frederic Lemoine Date: Mon, 3 May 2021 12:55:10 +0200 Subject: [PATCH] Updated doc for --ignore-identical --- docs/commands/append.md | 20 ++++----- docs/commands/consensus.md | 24 +++++------ docs/commands/extract.md | 20 ++++----- docs/commands/mask.md | 20 ++++----- docs/commands/revcomp.md | 20 ++++----- docs/commands/sample.md | 88 +++++++++++++++++++------------------- docs/commands/split.md | 20 ++++----- docs/commands/stats.md | 20 ++++----- docs/commands/subsites.md | 20 ++++----- docs/commands/translate.md | 20 ++++----- docs/commands/transpose.md | 20 ++++----- 11 files changed, 146 insertions(+), 146 deletions(-) diff --git a/docs/commands/append.md b/docs/commands/append.md index cda4c2c..39b7001 100644 --- a/docs/commands/append.md +++ b/docs/commands/append.md @@ -34,16 +34,16 @@ Flags: -o, --output string Alignment output file (default "stdout") Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` #### Examples diff --git a/docs/commands/consensus.md b/docs/commands/consensus.md index 91002dc..fe030ca 100644 --- a/docs/commands/consensus.md +++ b/docs/commands/consensus.md @@ -20,18 +20,18 @@ Flags: -o, --output string Alignment output file (default "stdout") Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --ignore-gaps Ignore gaps (except if only gaps on the column) - --ignore-n Ignore Ns (except if only N on the column) - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --ignore-gaps Ignore gaps (except if only gaps on the column) + --ignore-n Ignore Ns (except if only N on the column) + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` #### Examples diff --git a/docs/commands/extract.md b/docs/commands/extract.md index 849dc38..5a646e1 100644 --- a/docs/commands/extract.md +++ b/docs/commands/extract.md @@ -57,16 +57,16 @@ Flags: --translate int Wether the extracted sequence will be translated (only if input alignment is nucleotide). <0: No translation, 0: Std code, 1: Vertebrate mito, 2: Invertebrate mito (default -1) Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` #### Examples diff --git a/docs/commands/mask.md b/docs/commands/mask.md index f8f390a..01d0966 100644 --- a/docs/commands/mask.md +++ b/docs/commands/mask.md @@ -60,16 +60,16 @@ Flags: (start and length are ignored) Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` #### Examples diff --git a/docs/commands/revcomp.md b/docs/commands/revcomp.md index 300abe0..5bb42ca 100644 --- a/docs/commands/revcomp.md +++ b/docs/commands/revcomp.md @@ -22,16 +22,16 @@ Flags: --unaligned Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored) Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` diff --git a/docs/commands/sample.md b/docs/commands/sample.md index b04ae4d..66ae6b6 100644 --- a/docs/commands/sample.md +++ b/docs/commands/sample.md @@ -22,17 +22,17 @@ Flags: -h, --help help for sample Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta - --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta + --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) ``` * seqs command ``` @@ -47,17 +47,17 @@ Flags: --unaligned Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored) Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta - --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta + --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) ``` * sites command @@ -73,17 +73,17 @@ Flags: -o, --output string Alignment output file (default "stdout") Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta - --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta + --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) ``` * rarefy command @@ -100,17 +100,17 @@ Flags: --unaligned Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored) Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta - --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta + --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) ``` #### Examples diff --git a/docs/commands/split.md b/docs/commands/split.md index c4ca490..bd47f72 100644 --- a/docs/commands/split.md +++ b/docs/commands/split.md @@ -21,16 +21,16 @@ Flags: --partition string File containing definition of the partitions (default "none") Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string int Alignment input file (default "stdin") + --auto-detect int Auto detects input format (overrides -p, -x and -u) + -u, --clustal int Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict int Strict phylip input format (only used with -p) + -x, --nexus int Alignment is in nexus? default fasta + --no-block int Write Phylip sequences without space separated blocks (only used with -p) + --one-line int Write Phylip sequences on 1 line (only used with -p) + --output-strict int Strict phylip output format (only used with -p) + -p, --phylip int Alignment is in phylip? default fasta ``` #### Examples diff --git a/docs/commands/stats.md b/docs/commands/stats.md index 5af2134..2250f03 100644 --- a/docs/commands/stats.md +++ b/docs/commands/stats.md @@ -88,16 +88,16 @@ Available Commands: taxa Prints index (position) and name of taxa of the alignment file Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` #### Examples diff --git a/docs/commands/subsites.md b/docs/commands/subsites.md index 8016f90..543d905 100644 --- a/docs/commands/subsites.md +++ b/docs/commands/subsites.md @@ -74,16 +74,16 @@ Flags: --sitefile string File with positions of sites to select (one perline) (default "none") Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` diff --git a/docs/commands/translate.md b/docs/commands/translate.md index 1d815d4..997dbf1 100644 --- a/docs/commands/translate.md +++ b/docs/commands/translate.md @@ -33,16 +33,16 @@ Flags: --unaligned Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored) Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ``` diff --git a/docs/commands/transpose.md b/docs/commands/transpose.md index fc91d4d..44247fc 100644 --- a/docs/commands/transpose.md +++ b/docs/commands/transpose.md @@ -17,16 +17,16 @@ Flags: -o, --output string Output transposed alignment (default "stdout") Global Flags: - -i, --align string Alignment input file (default "stdin") - --auto-detect Auto detects input format (overrides -p, -x and -u) - -u, --clustal Alignment is in clustal? default fasta - --ignore-identical Ignore duplicated sequences that have the same name and same sequences - --input-strict Strict phylip input format (only used with -p) - -x, --nexus Alignment is in nexus? default fasta - --no-block Write Phylip sequences without space separated blocks (only used with -p) - --one-line Write Phylip sequences on 1 line (only used with -p) - --output-strict Strict phylip output format (only used with -p) - -p, --phylip Alignment is in phylip? default fasta + -i, --align string Alignment input file (default "stdin") + --auto-detect Auto detects input format (overrides -p, -x and -u) + -u, --clustal Alignment is in clustal? default fasta + --ignore-identical int Ignore duplicated sequences that have the same name and same sequences + --input-strict Strict phylip input format (only used with -p) + -x, --nexus Alignment is in nexus? default fasta + --no-block Write Phylip sequences without space separated blocks (only used with -p) + --one-line Write Phylip sequences on 1 line (only used with -p) + --output-strict Strict phylip output format (only used with -p) + -p, --phylip Alignment is in phylip? default fasta ```