From 0056336d4b245064a23e5b40197b29607fb1fe56 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 25 Feb 2021 07:19:54 +1000 Subject: [PATCH] v0.6.1 --- docs/coverm-cluster.html | 4 ++-- docs/coverm-contig.html | 25 +++++++++++++------------ docs/coverm-filter.html | 21 +++++++++++---------- docs/coverm-genome.html | 25 +++++++++++++------------ docs/coverm-make.html | 11 ++++++----- 5 files changed, 45 insertions(+), 41 deletions(-) diff --git a/docs/coverm-cluster.html b/docs/coverm-cluster.html index 7f38e68..65c54a5 100644 --- a/docs/coverm-cluster.html +++ b/docs/coverm-cluster.html @@ -63,7 +63,7 @@
coverm cluster usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-12-11 (coverm 0.6.0) +2021-02-25 (coverm 0.6.1)
@@ -90,7 +90,7 @@

NAME

-

coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.6.0)

+

coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.6.1)

SYNOPSIS

diff --git a/docs/coverm-contig.html b/docs/coverm-contig.html index a2289d1..f066792 100644 --- a/docs/coverm-contig.html +++ b/docs/coverm-contig.html @@ -63,7 +63,7 @@
coverm contig usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-12-11 (coverm 0.6.0) +2021-02-25 (coverm 0.6.1)
@@ -84,7 +84,7 @@
  • COVERAGE CALCULATION OPTIONS
  • OUTPUT
  • GENERAL OPTIONS
    • -
  • FREQUENTLY ASKED QUESTIONS
    • +
  • FREQUENTLY ASKED QUESTIONS (FAQ)
  • EXIT STATUS
  • EXAMPLES
  • AUTHOR
    • @@ -95,7 +95,7 @@

    NAME

    -

    coverm contig - Calculate read coverage per-contig (version 0.6.0)

    +

    coverm contig - Calculate read coverage per-contig (version 0.6.1)

    SYNOPSIS

    @@ -223,13 +223,13 @@

    ALIGNMENT THRESHOLDING

    --min-read-percent-identity FLOAT
    -

    Exclude reads by overall percent identity e.g. 0.95 for 95%. [default: 0.0]

    +

    Exclude reads by overall percent identity e.g. 95 for 95%. [default: 0]

    --min-read-aligned-percent FLOAT
    -

    Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. [default: 0.0]

    +

    Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. [default: 0]

    @@ -241,13 +241,13 @@

    ALIGNMENT THRESHOLDING

    --min-read-percent-identity-pair FLOAT
    -

    Exclude pairs by overall percent identity e.g. 0.95 for 95%. Implies --proper-pairs-only. [default: 0.0]

    +

    Exclude pairs by overall percent identity e.g. 95 for 95%. Implies --proper-pairs-only. [default: 0]

    --min-read-aligned-percent-pair FLOAT
    -

    Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: 0.0]

    +

    Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: 0]

    @@ -323,7 +323,7 @@

    COVERAGE CALCULATION OPTIONS

    --min-covered-fraction FRACTION
    -

    Genomes with less coverage than this reported as having zero coverage. [default: 0.10]

    +

    Genomes with less coverage than this reported as having zero coverage. [default: 10]

    @@ -335,13 +335,13 @@

    COVERAGE CALCULATION OPTIONS

    --trim-min FRACTION
    -

    Remove this smallest fraction of positions when calculating trimmed_mean [default: 0.05]

    +

    Remove this smallest fraction of positions when calculating trimmed_mean [default: 5]

    --trim-max FRACTION
    -

    Maximum fraction for trimmed_mean calculations [default: 0.95]

    +

    Maximum fraction for trimmed_mean calculations [default: 95]

    @@ -415,9 +415,10 @@

    GENERAL OPTIONS

    -
    -

    FREQUENTLY ASKED QUESTIONS

    +
    +

    FREQUENTLY ASKED QUESTIONS (FAQ)

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified? Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.

    EXIT STATUS

    diff --git a/docs/coverm-filter.html b/docs/coverm-filter.html index 357a86e..818637c 100644 --- a/docs/coverm-filter.html +++ b/docs/coverm-filter.html @@ -63,7 +63,7 @@
    coverm filter usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-12-11 (coverm 0.6.0) +2021-02-25 (coverm 0.6.1)
    @@ -79,7 +79,7 @@
  • FLAGS
  • OPTIONS
  • ALIGNMENT THRESHOLDING
    • -
  • FREQUENTLY ASKED QUESTIONS
    • +
  • FREQUENTLY ASKED QUESTIONS (FAQ)
  • EXIT STATUS
  • EXAMPLES
  • AUTHOR
    • @@ -90,7 +90,7 @@

    NAME

    -

    coverm filter - Threshold alignments with insufficient identity (version 0.6.0)

    +

    coverm filter - Threshold alignments with insufficient identity (version 0.6.1)

    SYNOPSIS

    @@ -168,13 +168,13 @@

    ALIGNMENT THRESHOLDING

    --min-read-percent-identity FLOAT
    -

    Exclude reads by overall percent identity e.g. 0.95 for 95%. [default: 0.0]

    +

    Exclude reads by overall percent identity e.g. 95 for 95%. [default: 0]

    --min-read-aligned-percent FLOAT
    -

    Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. [default: 0.0]

    +

    Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. [default: 0]

    @@ -186,13 +186,13 @@

    ALIGNMENT THRESHOLDING

    --min-read-percent-identity-pair FLOAT
    -

    Exclude pairs by overall percent identity e.g. 0.95 for 95%. Implies --proper-pairs-only. [default: 0.0]

    +

    Exclude pairs by overall percent identity e.g. 95 for 95%. Implies --proper-pairs-only. [default: 0]

    --min-read-aligned-percent-pair FLOAT
    -

    Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: 0.0]

    +

    Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: 0]

    @@ -208,9 +208,10 @@

    ALIGNMENT THRESHOLDING

    -
    -

    FREQUENTLY ASKED QUESTIONS

    +
    +

    FREQUENTLY ASKED QUESTIONS (FAQ)

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified? Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.

    EXIT STATUS

    @@ -239,7 +240,7 @@

    EXAMPLES

    $ coverm filter --bam-files input.bam --output-bam filtered.bam --min-read-aligned-length 50

    Filter inverse: Keep alignments that have <95% alignment identity and those which do map at all. Note that the output BAM file will likely records that are still mapped, but align with < 95% identity. Use 16 threads for output compression
    -

    $ coverm filter -b input.bam -o inverse_filtered.bam --inverse --min-read-percent-identity 0.95 --threads 16

    +

    $ coverm filter -b input.bam -o inverse_filtered.bam --inverse --min-read-percent-identity 95 --threads 16

    diff --git a/docs/coverm-genome.html b/docs/coverm-genome.html index 0ecdddf..450207f 100644 --- a/docs/coverm-genome.html +++ b/docs/coverm-genome.html @@ -63,7 +63,7 @@
    coverm genome usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-12-11 (coverm 0.6.0) +2021-02-25 (coverm 0.6.1)
    @@ -85,7 +85,7 @@
  • COVERAGE CALCULATION OPTIONS
  • OUTPUT
  • GENERAL OPTIONS
    • -
  • FREQUENTLY ASKED QUESTIONS
    • +
  • FREQUENTLY ASKED QUESTIONS (FAQ)
  • EXIT STATUS
  • EXAMPLES
  • AUTHOR
    • @@ -96,7 +96,7 @@

    NAME

    -

    coverm genome - Calculate read coverage per-genome (version 0.6.0)

    +

    coverm genome - Calculate read coverage per-genome (version 0.6.1)

    SYNOPSIS

    @@ -386,13 +386,13 @@

    ALIGNMENT THRESHOLDING

    --min-read-percent-identity FLOAT
    -

    Exclude reads by overall percent identity e.g. 0.95 for 95%. [default: 0.0]

    +

    Exclude reads by overall percent identity e.g. 95 for 95%. [default: 0]

    --min-read-aligned-percent FLOAT
    -

    Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. [default: 0.0]

    +

    Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. [default: 0]

    @@ -404,13 +404,13 @@

    ALIGNMENT THRESHOLDING

    --min-read-percent-identity-pair FLOAT
    -

    Exclude pairs by overall percent identity e.g. 0.95 for 95%. Implies --proper-pairs-only. [default: 0.0]

    +

    Exclude pairs by overall percent identity e.g. 95 for 95%. Implies --proper-pairs-only. [default: 0]

    --min-read-aligned-percent-pair FLOAT
    -

    Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: 0.0]

    +

    Exclude reads by percent aligned bases e.g. 95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: 0]

    @@ -486,7 +486,7 @@

    COVERAGE CALCULATION OPTIONS

    --min-covered-fraction FRACTION
    -

    Genomes with less coverage than this reported as having zero coverage. [default: 0.10]

    +

    Genomes with less coverage than this reported as having zero coverage. [default: 10]

    @@ -498,13 +498,13 @@

    COVERAGE CALCULATION OPTIONS

    --trim-min FRACTION
    -

    Remove this smallest fraction of positions when calculating trimmed_mean [default: 0.05]

    +

    Remove this smallest fraction of positions when calculating trimmed_mean [default: 5]

    --trim-max FRACTION
    -

    Maximum fraction for trimmed_mean calculations [default: 0.95]

    +

    Maximum fraction for trimmed_mean calculations [default: 95]

    @@ -578,9 +578,10 @@

    GENERAL OPTIONS

    -
    -

    FREQUENTLY ASKED QUESTIONS

    +
    +

    FREQUENTLY ASKED QUESTIONS (FAQ)

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified? Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.

    EXIT STATUS

    diff --git a/docs/coverm-make.html b/docs/coverm-make.html index b86d98b..79964fe 100644 --- a/docs/coverm-make.html +++ b/docs/coverm-make.html @@ -63,7 +63,7 @@
    coverm make usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-12-11 (coverm 0.6.0) +2021-02-25 (coverm 0.6.1)
    @@ -81,7 +81,7 @@
  • MAPPING ALGORITHM OPTIONS
  • OUTPUT
  • GENERAL OPTIONS
    • -
  • FREQUENTLY ASKED QUESTIONS
    • +
  • FREQUENTLY ASKED QUESTIONS (FAQ)
  • EXIT STATUS
  • EXAMPLES
  • AUTHOR
    • @@ -92,7 +92,7 @@

    NAME

    -

    coverm make - Generate BAM files through mapping (version: 0.6.0)

    +

    coverm make - Generate BAM files through mapping (version: 0.6.1)

    SYNOPSIS

    @@ -246,9 +246,10 @@

    GENERAL OPTIONS

    -
    -

    FREQUENTLY ASKED QUESTIONS

    +
    +

    FREQUENTLY ASKED QUESTIONS (FAQ)

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified? Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.

    EXIT STATUS