[Debian-med-packaging] changes to nanopolish packaging

[Afif Elghraoui]

Hi, Steffen,

I am just about to upload the latest nanopolish release and had a couple
questions about your changes. First, you have this patch:

```
Author: Steffen Moeller
Last-Updated: 2017-09-16 02:14:07 +0200
Description: Do not ignore return values of samtool functions

--- nanopolish.orig/src/alignment/nanopolish_eventalign.cpp
+++ nanopolish/src/alignment/nanopolish_eventalign.cpp
@@ -229,7 +229,7 @@

 void emit_sam_header(samFile* fp, const bam_hdr_t* hdr)
 {
-    sam_hdr_write(fp, hdr);
+    int r = sam_hdr_write(fp, hdr);
 }

 std::string cigar_ops_to_string(const std::vector<uint32_t>& ops)
@@ -368,7 +368,7 @@
     int stride = alignments.front().event_idx <
alignments.back().event_idx ? 1 : -1;
     bam_aux_append(event_record, "ES", 'i', 4,
reinterpret_cast<uint8_t*>(&stride));

-    sam_write1(fp, base_hdr, event_record);
+    int r = sam_write1(fp, base_hdr, event_record);
     bam_destroy1(event_record); // automatically frees malloc'd segment
 }
```

Despite the patch description, it looks to me like the return code is
still ignored. While it's now not being thrown away, it's not actually
being checked. Do you want to instead report this as an issue upstream?

My second question is about the -flto flag you added to the build. Is
that something we should be adding to more of our packages?

Thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name