Add output of only count of constant sites #84
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I did not add a test for this code because I do not quite understand how the testing system works. |
tseemann
reviewed
Oct 22, 2019
src/alignment-file.c
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| gzFile fp; | ||
| int base_counts[] = {0, 0, 0, 0}; | ||
| /* array below allows quick mapping of A, C, T and G characters to indices in base_counts array */ | ||
| int char_to_base_count_index[] = {-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, -1, 1, -1, -1, -1, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 3}; |
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Could this be const int ?
tseemann
reviewed
Oct 22, 2019
| } | ||
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| if (output_constant_site_counts) | ||
| printf("%d,%d,%d,%d\n", base_counts[0], base_counts[1], base_counts[2], base_counts[3]); |
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Just confirming these in A C G T order?
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I was discussing with some colleagues computing the count of constant sites in an alignment (for input to the
-fconstoption of IQ-TREE) when @tseemann suggested adding a routine tosnp-sites. This PR adds that routine using the-Cflag. The version number is not changed in this patch but feel free to merge the code if you think it is useful.