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No, they are not at all the same thing. An archive is just that. A collection of object files that can be statically linked to your executable. Shared objects are dynamically linked at runtime. They...

Just because a liib is updated ... you do not have to recompile at all if your static binary is working fine.

In addition, shared libs can introduce major IT security issues.

There is "No Free...

rpath is actually a linker option rather then a compiler option. gcc passes it to ld.



Well, th estandard way to use shared objects (.so) is to install them in the system directories used for...

If you link to a shared library intead of the archive it's a little more complicted. If the shared library isn't installed in a directory know to the loader then you need to tell it where to find it....

No. Each folder requires a -L entry.






I presumed htslib-1.10-2 was your library. The -l option is for the library itself. If the library is libhts.so then use -lhts





I'll have a...

Undefined references means the compiler can't find compiled code for functions being called. If you want to use a subset of the library then you'll have to compile and link all the files used by the...

First, I suggest when troubleshooting, you should:

Use the full path name to file, not relative path name. This will insure there are no strange, unseen PATH issues. For example:

gcc -Wall...

Thank you, Jim. That's a great tutorial.

In case this helps other newbies, I moved the getstring function to a separate file containing custom functions. Also, I changed getstring's logic to go...

realloc() is not guaranteed to reallocate in situ, which is why you do
str = realloc(str, mem); rather than realloc(str, mem); The next_read variable should be reset with something like next_read =...

BTW in many cases a trim function comes in handy.
For example, the fuzzy strstr() that can match a portion of the string can be replaced with an exact strcmp()
...
//...

The empty line prints str1.
Because it was not matched in scanf() it has the value from the previous line - therefore the str1= assignment,
should set it to "" with one of
str1[0]=0 or...

The str1 variable is too small. "sample10" is 8 characters, so str1 must have 8+1=9 bytes wide at least.
char name[256]; //1st part (key part) parsed from each line[]
char str1[12]; ...

The code that you provided stops at line 8 with exit 1:
...
printf("%s: %s\n", name, str1); //puts() always adds newline at the end of the string
//printf("%d\n", i);
...

For me it works: the red phrases land in the blue variables.
But there can be trailing spaces in name because %[^:] matches up to the :

1) It looks like vgersh99 has already shown you how to expand shell variables for use in awk. Note, however, that his code will append to your two output files; not replace them if they already...

MY_DIR="/storage/tmp"
awk -v myDir="${MY_DIR}" '{if ($1 == "aaa") out=(myDir "/group_a.gtf"); else if ($7 == "bbb") out=(myDir "/group_b.gtf"); print >> out;close(out)} ' infile

awk version you could try:
awk 'BEGIN{FS=RS; RS=">"; ORS=""} FNR>1{A[$1]=RS $0} END{for(i in A) print A[i]}' file1 file2

note: ensure that there are no excess trailing spaces as is the case with...

May I paraphrase your request: You want file2's sequences to prevail and file1's sequences inserted only if there's no equivalent in file2. If so, try
tr $'\n>' $' \n' <file1| grep -vf <(sed -n...

not sure if I follow your samples and the desired output, but I think you might want this.

awk -f dinesh.awk file2 file1 where dinesh.awk is:

FNR==NR {
if (FNR%2)
head=$0
else
...

Parallel is not a go-faster button for files. Unless your CPU is maxing out, there's no benefit.

GNU parallel is just doing individual files like you were doing anyway. It has to, lacking magic...

Actually this is a very interesting problem. It is hard simulate without actually create some terabytes of files that are similar in size to what you have to process, therefore, before i start to...

How about something more like:
LIST1=/what/ever/you/want
OUTPUT1=raw_reads_count.table1

while read -r f
do ( linecount=$(zcat ${f}_R1.fq.gz | wc -l)
printf '%s\t%s\n' "$f" "$linecount" >>...

How about
{ echo -n $f" "; zcat ${f}_R1.fq.gz | wc -l; } >> raw_reads_count.table1 &
Should that fail, write to single files in sequence, then, after the loop, concatenate the files.

Buffering will make a mess of this, bundling arbitrary blocks into one write. These arbitrary blocks don't care much where lines begin and end. Long enough lines could conceivably take more than...

The risk of strcpy is this:

char buf[8]; // Only room for 8 characters
char very_important_variable_touch_and_the_world_explodes=42;

// More than 8 characters, where does the rest go?...