重新注意这些参数，“
(Hic
) [scb3201@ln137%bscc
-a6 ~]$ juicer
Usage
: juicer <command> <arguments>
Version
: 1
.2
.2
Command
: pre generate files compatible
with Juicebox
toolset
post generate assembly files after Juicebox curation
(Hic
) [scb3201@ln137%bscc
-a6 ~]$ juicer pre
[E
::main_pre] missing input
: three positional options required
Usage
: juicer pre [options] <hic
.bed>|<hic
.bam>|<hic
.pa5>|<hic
.bin> <scaffolds
.agp> <contigs
.fa
.fai>
Options
:
-a preprocess for assembly mode
-q INT minimum mapping quality [10]
-o STR output file prefix
(required for '
-a' mode
) [st
dout]
--file
-type STR input file type BED|BAM|PA5|BIN, file name extension is ignored if set
--version show version number
(Hic
) [scb3201@ln137%bscc
-a6 ~]$ juicebox_assembly_converter
.py
usage
: juicebox_assembly_converter
.py [
-h]
-a ASSEMBLY
-f FASTA [
-p PREFIX] [
-c] [
-s] [
-v]
juicebox_assembly_converter
.py
: error
: the following arguments are required
: -a/
--assembly,
-f/
--fasta
(Hic
) [scb3201@ln137%bscc
-a6 Hic]$ juicer post
[E
::main_post] missing input
: three positional options required
Usage
: juicer post [options] <review
.assembly> <lif
tover
.agp> <contigs
.fa[
.fai]>
Options
:
-o STR output file prefix
(required for scaffolds FASTA output
) [st
dout]
--seq
-ctype STR AGP output sequence component type [W]
--gap
-ctype STR AGP output gap component type [U]
--gap
-link STR AGP output gap linkage evidence [proximity_ligation]
--gap
-size INT AGP output gap size between sequence component [100]
--version show version number
(Hic
) [scb3201@ln137%bscc
-a6 Hic]$ /public1/home/scb3201/anaconda3/envs/Hic/share/juicer
-1
.6
-0/juicer_
tools
-h
WARNING
: sun
.reflect
.Reflection
.getCallerClass is not supported
. This will impact performance
.
WARN [2025
-12-08T16
:37
:25,594] [Globals
.java
:138] [main] Development mode is enabled
Juicer
Tools Version 1
.22
.01
Usage
:
dump <observed/oe> <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr1>[
:x1
:x2] <chr2>[
:y1
:y2] <BP/FRAG> <binsize> [outfile]
dump <norm/expected> <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr> <BP/FRAG> <binsize> [outfile]
dump <loops/
domains> <hicFile URL> [outfile]
pre [options] <infile> <outfile> <genomeID>
addNorm <input_HiC_file> [input_
vector_file]
pearsons [
-p] <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr> <BP/FRAG> <binsize> [outfile]
eigen
vector -p <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr> <BP/FRAG> <binsize> [outfile]
apa <hicFile
(s
)> <PeaksFile> <SaveFolder>
arrowhead <hicFile
(s
)> <output_file>
hiccups <hicFile> <outputDirec
tory>
hiccupsdiff <firstHicFile> <secondHicFile> <firstLoopList> <secondLoopList> <outputDirec
tory>
validate <hicFile>
-h,
--help print help
-v,
--verbose verbose mode
-V,
--version print version
Type juicer_
tools <commandName> for more detailed usage instructions
(Hic
) [scb3201@ln137%bscc
-a6 Hic]$ /public1/home/scb3201/anaconda3/envs/Hic/share/juicer
tools/juicer_
tools
-h
WARNING
: sun
.reflect
.Reflection
.getCallerClass is not supported
. This will impact performance
.
WARN [2025
-12-08T16
:37
:45,685] [Globals
.java
:138] [main] Development mode is enabled
Juicer
Tools Version 2
.20
.00
Usage
:
dump <observed/oe> <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr1>[
:x1
:x2] <chr2>[
:y1
:y2] <BP/FRAG> <binsize> [outfile]
dump <norm/expected> <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr> <BP/FRAG> <binsize> [outfile]
dump <loops/
domains> <hicFile URL> [outfile]
pre [options] <infile> <outfile> <genomeID>
addNorm <input_HiC_file> [input_
vector_file]
pearsons [
-p] <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr> <BP/FRAG> <binsize> [outfile]
eigen
vector -p <NONE/VC/VC_SQRT/KR> <hicFile
(s
)> <chr> <BP/FRAG> <binsize> [outfile]
apa <hicFile
(s
)> <PeaksFile> <SaveFolder>
arrowhead <hicFile
(s
)> <output_file>
hiccups <hicFile> <outputDirec
tory>
hiccupsdiff <firstHicFile> <secondHicFile> <firstLoopList> <secondLoopList> <outputDirec
tory>
validate <hicFile>
-h,
--help print help
-v,
--verbose verbose mode
-V,
--version print version
Type juicer_
tools <commandName> for more detailed usage instructions
(Hic
) [scb3201@ln137%bscc
-a6 Hic]$ /public1/home/scb3201/anaconda3/envs/Hic/share/juicer
-1
.6
-0/juicer_
tools pre
WARNING
: sun
.reflect
.Reflection
.getCallerClass is not supported
. This will impact performance
.
WARN [2025
-12-08T16
:40
:00,498] [Globals
.java
:138] [main] Development mode is enabled
Usage
: juicer_
tools pre [options] <infile> <outfile> <genomeID>
: -d only calculate intra chromosome
(diagonal
) [false]
: -f <restriction site file> calculate fragment map
: -m <int> only write cells
with count above threshold m [0]
: -q <int> filter by MAPQ score greater than or equal
to q [not set]
: -c <chromosome ID> only calculate map on specific chromosome [not set]
: -r <comma
-separated list of resolutions> Only calculate specific resolutions [not set]
: -t <tmpDir> Set a temporary direc
tory for writing
: -s <statistics file> Add the text statistics file
to the Hi
-C file header
: -g <graphs file> Add the text graphs file
to the Hi
-C file header
: -n
Don't normalize the matrices
: -z <
double> scale fac
tor for hic file
: -a <1, 2, 3, 4, 5> filter based on inner, outer, left
-left, right
-right, tandem pairs respectively
: --ran
domize_position ran
domize positions between fragment sites
: --ran
dom_seed <long> for seeding ran
dom number genera
tor
: --frag_site_maps <fragment site files> for ran
domization
: -k normalizations
to include
: -j number of CPU threads
to use
: --threads <int> number of threads
: --mndindex <filepath>
to mnd chr block indices
(Hic
) [scb3201@ln137%bscc
-a6 Hic]$ /public1/home/scb3201/anaconda3/envs/Hic/share/juicer
tools/juicer_
tools pre
WARNING
: sun
.reflect
.Reflection
.getCallerClass is not supported
. This will impact performance
.
WARN [2025
-12-08T16
:40
:28,943] [Globals
.java
:138] [main] Development mode is enabled
Usage
: juicer_
tools pre [options] <infile> <outfile> <genomeID>
: -d only calculate intra chromosome
(diagonal
) [false]
: -f <restriction site file> calculate fragment map
: -m <int> only write cells
with count above threshold m [0]
: -q <int> filter by MAPQ score greater than or equal
to q [not set]
: -c <chromosome ID> only calculate map on specific chromosome [not set]
: -r <comma
-separated list of resolutions> Only calculate specific resolutions [not set]
: -t <tmpDir> Set a temporary direc
tory for writing
: -s <statistics file> Add the text statistics file
to the Hi
-C file header
: -g <graphs file> Add the text graphs file
to the Hi
-C file header
: -n
Don't normalize the matrices
: -z <
double> scale fac
tor for hic file
: -a <1, 2, 3, 4, 5> filter based on inner, outer, left
-left, right
-right, tandem pairs respectively
: --ran
domize_position ran
domize positions between fragment sites
: --ran
dom_seed <long> for seeding ran
dom number genera
tor
: --frag_site_maps <fragment site files> for ran
domization
: -k normalizations
to include
: -j number of CPU threads
to use
: --threads <int> number of threads
: --mndindex <filepath>
to mnd chr block indices
: --conserve
-ram will minimize RAM usage
: --check
-ram
-usage will check ram requirements prior
to running
: --shell how
to execute shell
(sh, bash, zsh, etc
); default
: sh”并根据这些参数重新核对脚本
本文讨论了C++中vector容器的安全使用方法，特别是避免在使用引用和指针访问vector元素时出现的问题。当对vector进行扩展操作如push_back、reserve或resize时，可能导致原有引用和指针失效。
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