bison | Bisulfite alignment on nodes of a cluster
kandi X-RAY | bison Summary
kandi X-RAY | bison Summary
If you use Bison in your work please site the following: Ryan D.P. and Ehninger D. Bison: bisulfite alignment on nodes of a cluster. BMC Bioinformatics 2014, Oct 18;15(1):337.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of bison
bison Key Features
bison Examples and Code Snippets
exptData <- SimpleList(Sequencer="Some sequencer", Year="2014") #This is just descriptive information
M <- as.matrix(read.delim("chr17.M", header=T))
Cov <- as.matrix(read.delim("chr17.Cov", header=T))
bed <- read.delim("chr17.bed", heade
M <- as.matrix(read.delim("Chr17.M", header=T))
Cov <- as.matrix(read.delim("Chr17.Cov", header=T))
bed <- read.delim("Chr17.bed", header=F)
#Remember that BED and bedGraph files are 0-based!
gr <- GRanges(seqnames=Rle(bed$V1),ranges=IRan
fai <- read.delim("genome.fa.fai", header=F)
chromosome_lengths <- fai$V2
names(chromosome_lengths) <- fai$V1
d <- readMethylome("file.MethylSeekR", chromosome_lengths)
Community Discussions
Trending Discussions on bison
QUESTION
I'm attempting to create a reentrant parser using C++ with flex and bison. I'm also using a driver class Driver
. I'm getting the error 'yyscanner' : undeclared identifier
on the lex side of things. I think it has something to do with the reentrant option in flex, which is strange since I would have assumed that driver
would have been used in it's place, since I declare yylex
as yylex(Driver& driver)
in driver.h
. Is there anything I've done wrong in my code below to get this error message? Any help would be much appreciated.
parser.y
...ANSWER
Answered 2021-Jun-12 at 23:55If you generate a reentrant scanner, you must define its prototype to include a parameter named yyscanner
of type yyscan_t
. And you need to call the scanner with that argument. You cannot substitute some type you have defined for the yyscan_t
argument, because your type does not include the data members which the flex-generated scanner uses. And you must use the name yyscanner
because that's how the code generated by Flex references the data members.
If you want a yylex
which only needs one argument, the "official" way to do that is to put your data members (or a pointer to them) into the "extra data" in the yyscan_t
. But it might be easier to just use two arguments.
QUESTION
I have a project which has a docker-compose file and a Dockerfile. The project is open here GitHub
I'm building a demo project with:
- Traefik
- Snort 3
- A NodeJS API dummy for testing
The issue is that in my Docker file I have a command like this to run on Snort
...ANSWER
Answered 2021-Jun-07 at 12:56Your entrypoint is conflicting with the command you want to run:
QUESTION
I'm trying to set up my environment to use Yocto's generated SDK to compile my out-of-tree module, but for some reason, I'm getting an error.
cp: cannot stat 'arch/arm/kernel/module.lds': No such file or directory
I'm using Poky distribution and meta-raspberrypi which is needed because I'm using the RPI ZeroW board. Apart from this everything works fine. I'm able to compile the entire image and load it on the board.
Here is the line I've added to local.conf
TOOLCHAIN_TARGET_TASK_append = " kernel-devsrc"
as I've found in the documentation.
Also below you can find the whole log from the compilation.
...ANSWER
Answered 2021-Jun-07 at 11:16Missing the module.lds file in the latest kernel. Apply the following source code as a patch in the kernel and build the image.
QUESTION
I am writing a simple calculator in which an expression can be reduced to a statement, or list of statements. If a bad expression triggers a syntax error, I try to catch it with a production rule and then ignore it by giving the rule no actions. However, I believe this still reduces to a stmt_list
despite it not being a valid statement.
Is there a way to make it simply ignore tokens matched with an error and prevent them from being reduced and used later?
The code below matches error ';'
and reduces it to a stmt_list
. It will then try to reduce that stmt_list
with a valid expression, but since the first production was never called this will trigger a memory exception. My objective is to have Bison literally do nothing if an error is matched, such that a later valid expression can be the first reduction to stmt_list
.
ANSWER
Answered 2021-Jun-07 at 03:23If you supply no action for a rule, bison/yacc provides the default action $$ = $1
.
In fact, you are not providing no action. You are providing an explicit action which does nothing. As it happens, if you use the C template, the parser will still perform the default action. In other templates, an action which does not assign a value to $$
might provoke a warning during parser generation. But it certainly won't modify your data structures so as to nullify the action. It can't know what that means. If you know, you should write it as the action :-) .
It's not 100% clear to me why you are keeping the results of the evaluations in a fixed-size dynamically-allocated array. You make no attempt to detect when the array fills up, so it's entirely possible that you'll end up overflowing the allocation and overwriting random memory. Moreover, using a global like this isn't usually a good idea because it prevents you from building more than one list at the same time. (For example, if you wanted to implement function calls, since a function's arguments are also a list of expressions.)
On the whole, it's better to put the implementation of the expanding expression list in a simple API which is implemented elsewhere. Here, I'm going to assume that you've done that; for specificity, I'll assume the following API (although it's just one example):
QUESTION
I am using flex and bison on windows from this repository along with Visual Studio 2019 to produce a small calculator application.
Earlier I enabled bison debug messages through the build properties in VS. I've now turned it off, cleaned and rebuilt the project but the debug messages are still persisting in the calculator. I have also tried a number of other ways to explicitly disable it, such as setting YYDEBUG
to 0 and %define parse.trace false
.
Flex
...ANSWER
Answered 2021-May-30 at 23:36It seems it was lex tracing, which I've been able to disable through the bison/yacc input file.
In the definitions code, add:
extern int yy_flex_debug;
In your main method, add:
yy_flex_debug = 0;
QUESTION
I was having some trouble with Bison creating an operator as such:
<-
= identity postfix operator with a low precedence to force evaluation of what's on the left first, e.g. 1+2<-*3
(equivalent (1+2)*3
) as well as ->
which is a prefix operator which does the same thing but to the right.
I was not able to get the syntax to work properly and tested with Python using - not False
, which resulted in a syntax error (in Python, -
has a greater precedence than not
). However, this is not a problem in C or C++, where -
and !
/not
have the same precedence.
Of course, the difference in precedence has nothing to do with the relationship between the 2 operators, only a relationship with other operators that result in the relative precedences between them.
Why is chaining prefix or postfix operators with different precedences a problem when parsing and how can implement the <-
and ->
operators while still having higher-precedence operators like !
, ++
, NOT
, etc.?
Obligatory Bison (this pattern is repeated for all operators, where copy
has greater precedence than post_unary
):
ANSWER
Answered 2021-May-25 at 03:45Ok, let me suggest a possible erroneous grammar based on your sketch:
QUESTION
So i am trying to make e lexical parsher using Flex Code with a bit of Bison.I keep getting a warning about my rules than cannot be matched and i cannot find any error.I have also searched what that warning means,but i think i haven't declared a similar rule again.So there is no chance i think that any other rule overpasses other rules and cannot be matched.I keep getting an error from line 83 which is {COMMA} {return COMMA;},till the end of my code and i dunno why.Any ideas?
...ANSWER
Answered 2021-May-23 at 16:13In your rules, {UNKNOWN_TOKEN}
appears very early. Since it matches any token of any length not containing whitespace, it will match the same tokens as any following rule (and possibly more characters as well). Since (f)lex always choses the first rule if more than one rule is possible, none of the rules after {UNKNOWN_TOKEN}
will ever match.
I suggest you use fewer macros. (Or no macros at all.) They are not contributing anything to your code. They only make it unnecessarily long, and they are confusing you (I think) because macro definitions are not rules and the order of macro definitions does not affect the match, only the order of the rules themselves.
There are some other errors as well. For example, [\+\+]
does not match ++
. It is a character class, so it matches precisely one character. The only character it can match is +
because repeated characters in a set don't change the set. (There is no need to backslash-escape +
in a character class either. Inside brackets most characters lose their special meaning.) What you meant was "++"
.
QUESTION
I am trying to make a C-like language using Flex/Bison. My problem is that I can't find a proper way to handle new lines. I have to ignore all new lines so I don't returnt them as a token to Bison because that would make the grammar rules so difficult to make but I am asked in some rules to make a mandatory change of line. For example:
Program "identifier" -> mandatory change of line
Function "identifier"("parameters") -> mandatory change of line
If I return \n as a token to flex then i have to put new lines in all of my grammar rules and that's surely not practical. I tried to make a variable work like a switch or something but it didn't quite work. Any help or suggestion?
...ANSWER
Answered 2021-May-17 at 13:22There is a pattern called trailing context you cant try : https://people.cs.aau.dk/~marius/sw/flex/Flex-Regular-Expressions.html
"identifier"/[\n]
"function-identifier"/[\n]
QUESTION
I have a svg generated by javascript and included inline in the HTML page. On top (above, higher z-index) of some hexes (polygons defined in SVG) I want to display an image.
I was able to do it adding a div containing the image with css position absolute and top/left/width in pixels.
But, with the data I have to display, that means adding 473 div for 39 different images (473 polygons out of ~10k need an image, 74 lines and 134 columns of hexes). The image represents the map of the world and the hexes can have about 40 different colors. You can see it here.
I was wondering if there was a solution to make that image appear on top of the hex, ideally in svg or in css? like adding a class to the polygon, or a style?
I have tried putting a style to a polygon and giving it a background-image, contain the image within the polygon, but the color of the polygon prevails on top.
Here is the code with:
- the first polygon of the first line with an image over it thanks to the div solution
- the last polygon of the second line with a CSS changing color into orange but failing to add an image on top of the orange (and even with fill:none !?)
ANSWER
Answered 2021-May-08 at 05:17You can achieve by setting the background into a pattern and set the style of fill as the pattern.
QUESTION
Hi I have some of the small programs, each of them will be compiled and run individually.
I was planning on using target specific variables to make the different programs, since it will be inherited recursively by target's prerequisites. Thus I could keep the dependency structure of compiled targets, and make the most use of duplicated commands.
The following is the current makefile:
...ANSWER
Answered 2021-May-10 at 15:17# $@ 表示目标文件
# $^ 表示所有的依赖文件
# $< 表示第一个依赖文件
# $? 表示比目标还要新的依赖文件列表
# Variables =====================================================================================
PHONY =
# Main*****************************************
proj = main
ifeq ($(proj),wc)
LEX_FILE = wc.l
else ifeq ($(proj),ab)
LEX_FILE = lex.l
BISON_FILE = yacc.y
else
LEX_FILE = lex.l
BISON_FILE = yacc.y
endif
BISON_OUT = $(subst .y,,$(BISON_FILE)).tab.c $(subst .y,,$(BISON_FILE)).tab.h
LEX_OUT = $(subst .l,,$(LEX_FILE)).yy.c
CFLAGS = -g -lfl
# Flex ==========================================================================================
$(LEX_OUT):$(LEX_FILE) $(BISON_OUT)
@echo $(BISON_FILE)
@echo $(BISON_OUT)
flex --outfile=$@ $<
# Bison =========================================================================================
$(BISON_OUT):$(BISON_FILE)
ifneq ($(BISON_FILE),)
@echo $(BISON_FILE)
bison -d $<
endif
# Run ===========================================================================================
$(proj).out:$(LEX_OUT) $(BISON_OUT)
ifneq ($(BISON_FILE),)
gcc $(CFLAGS) $(word 1,$^) $(word 2,$^) -o $@
else
gcc $(CFLAGS) $(word 1,$^) -o $@
endif
run:$(proj).out
./$<
PHONY += run run_wc
# Clean =========================================================================================
clean:
-rm *.out *.yy.c *.tab.h *.tab.c *.s
PHONY += clean
# PHONY =========================================================================================
.PHONY: $(PHONY)
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install bison
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page