bug fix: samtools merge --template-coordinate #1705
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The keys used to compare based on template coordinate were not being created as the input sorted BAMs were being merged
nh13
commented
Aug 25, 2022
| if (keys->n + n >= keys->m * keys->buffer_size) { | ||
| if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail; | ||
| } | ||
| lib_lookup = lookup_libraries(hout); |
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I am unsure of which header to use, so I picked the output one. I think that's correct, but it could use a second set of eyes.
nh13
commented
Aug 25, 2022
| @@ -1686,7 +1728,7 @@ static inline int heap_add_read(heap1_t *heap, int nfiles, samFile **fp, | |||
| if (in_mem[i - nfiles].from < in_mem[i - nfiles].to) { | |||
| size_t from = in_mem[i - nfiles].from; | |||
| heap->entry.bam_record = buf[from].bam_record; | |||
| if (g_sam_order == TemplateCoordinate) heap->entry.u.key = template_coordinate_keys_get(keys, from); | |||
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changes here and below are from #1703
nh13
commented
Aug 25, 2022
| @@ -1379,6 +1410,10 @@ int bam_merge_core2(SamOrder sam_order, char* sort_tag, const char *out, const c | |||
| heap->idx = idx++; | |||
| if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) { | |||
| heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag); | |||
| } else if (g_sam_order == TemplateCoordinate) { | |||
| template_coordinate_key_t *key = template_coordinate_keys_get(keys, heap->i); // get the next key to use | |||
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I think heap->i is the correct index, but could use another set of eyes.
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This includes the commit for the fix in #1703, so this should be merged only after that has been merged.
The keys used to compare based on template coordinate were not being created as the input sorted BAMs were being merged.
Tested via merging large sorted files that were created using the fix in #1703.