For this practice, I am struggling to catch the flow of the
strtok() is pretty simple once you know what it does, which is why it's so fast.
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The part I am still not sure is:
1) In the line with ">", the first field is stored as one string, except the '>' char which is a separator for each record (like RS in awk).
Which line of what now?
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2) All the rest of the field next to the ">" line are concatenated to have a single string. It is easy for printing, but to track them in memory with
I am not sure at all.
For example, the entry:
Onlyseq01 is picked up for key on the first line, the other part are discarded; from the second row of the entry all is concatenated: AGCTACGTACATCAGTCGTGTGATCGAGCGGG for value of the map (if I insist map be used!)
strtok() discards the spaces replacing them with NULL terminators. Instead of printing a space, the string ends early. This even lets it break it into a bunch of separate mini-strings without copying it anywhere or using any more memory.
Let me illustrate it. What does this code print?
This is all strtok does, change your spaces into NULs and tell you where it started.
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I seem to understand the syntax, as I can print out the individual field parsed, but do not know how to combine certain fields together if needed.
There's much less technically wrong with your programs now, most of your problems are innocent mistakes. But an innocent mistake with a pointer makes your program explode without even telling you where or why.
This leaves you trying to fix your program by wild guessing, which is incredibly frustrating. Let me help you out.
You can consider an assert to be a "controlled crash". This should take a lot of the mystery out of your programs because, unlike a segfault, it tells you exactly where and why it broke down. You can dump them wherever you want without changing your program logic.
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Maybe I should not say I understand the syntax.
How the pointer/reference is manipulated behind is the bottleneck for me to catch the whole point. Can you elaborate that? Thanks!
It might surprise you just how short a function strtok() is. Here's a simplified one for clarity:
Last edited by Corona688; 09-18-2014 at 07:52 PM..
Two questions related the movement of the pointer char *tok and for my planned string map of sequences.
With multiple strings as:
Using your my_strtok() function, it is easy to parse each string(char array) and print out on screen as the pointer moves forward.
Question 1: How to save (NOT print) concatenated strings in memory?
Of course string3 will be an empty one, and a master string
The reason I ask for "save" is for the manipulation of the variable char *tok.
I seem to be quite vague about this pointer in the stack or/and heap(if I am not too wrong with the two terms!?)
Question 2: How is the pointer char *tok (and probably some new pointers to save the concatenated strings) moving back and forth to have those individual concatenated strings and the master string?
Question 1: You worked that out pages ago, string += token; For std::string anyway. For C-strings, it means adding more to the end of an array, so you have to worry about whether there's room, etc.
Question 2: Follow the logic in the function. I've labelled the value of 'last' as green and the value of 'first' as red so you can see which one strtok is using when.
First case: You give it a new string:
You get the exact same pointer you put in. This makes sense -- strtok modifies the original and gives it back.
Second case: Getting an additional token from the previous string:
This time, we get the string from last. It was "def ghi" before, altered to "def\0gh" to split the token, then returned to us unchanged. last, on the other hand, is changed, now pointing to "def" (marked in purple.)
Last edited by Corona688; 09-19-2014 at 05:08 PM..
Is there any special reason you used char as delimiter for your function?
Whereas normal one is
I guess they are quite different in the background (to rewrite the source code) between the two, as ' ' is for char where " " for string. Yours uses single char as delimiter and the strtok() uses multiple char delimiters, right?
Is there any special reason you used char as delimiter for your function?
I made it as short as I could without calling any string.h functions.
Making it use a string would be a very simple change from (first[pos] != c) to (strchr(first[pos], t) == NULL) -- or a small loop, if written without strchr:
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Yours uses single char as delimiter and the strtok() uses multiple char delimiters, right?
Yes, it uses any of them. strtok(buf, "abe") is telling it "end the token when you find one or more of ANY of these characters". When breaking tokens on space, I also check for tabs, carriage returns, and newlines out of habit. That'll make it work even on the messiest text. (It also eats the newlines fgets includes in the lines it reads, a habit getline does not share.)
The real strtok will also strip off leading characters -- scanning " a b c d e " would find "a", "b", "c", "d", "e", while my "fake" strtok would find "", "a", "b", "c", "d", "e". Another little loop at the beginning would fix that.
Last edited by Corona688; 09-19-2014 at 09:02 PM..
Hi
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<logentry revision="21510">
<author>mantest</author>
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CHROM POS REF ALT 10_sample.bam 11_sample.bam 12_sample.bam 13_sample.bam 14_sample.bam 15_sample.bam 16_sample.bam
tg93 77 T C T T T T T
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