add warning flags to ig-sw

@matsen it would be great if we could add these flags to ig-sw: '-Wall', '-Wextra', '-pedantic' (as seen here.

You sounded like you're familiar enough with the code to try -- the signed/unsigned comparison warnings are potentially scary, but fixing them also terrifies me since I don't know anything about the code...

gcc -o ig_align.o -c -std=gnu99 -Ofast -Wall -Wextra -pedantic -I. -Itclap ig_align.c
ig_align.c:61:26: warning: ISO C does not allow extra ';' outside of a function [-Wpedantic]
 KSEQ_INIT(gzFile, gzread);
                          ^
In file included from ig_align.c:15:0:
ig_align.c: In function 'ks_sample_cdec_score':
ksort.h:256:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \
          ^
ig_align.c:127:1: note: in expansion of macro 'KSORT_INIT'
 KSORT_INIT(cdec_score, aln_t, __aln_score_lt)
 ^
ig_align.c: In function 'align_read':
ig_align.c:247:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < kv_size(result); i++)
                       ^
ig_align.c: In function 'write_sam_records':
ig_align.c:328:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (a.loc.qe + 1 != read->seq.l)
                      ^
gcc -o ksw.o -c -std=gnu99 -Ofast -Wall -Wextra -pedantic -I. -Itclap ksw.c
ksw.c: In function 'push_cigar':
ksw.c:464:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
                          ^
gcc -o kstring.o -c -std=gnu99 -Ofast -Wall -Wextra -pedantic -I. -Itclap kstring.c
kstring.c: In function 'kvsprintf':
kstring.c:15:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (l + 1 > s->m - s->l) {

psathyrella / partis

add warning flags to ig-sw #223