Outdated c++, needs considerable work

amos (3.1.0-1) UNRELEASED; urgency=low

  * Initial release (Closes: #897191).

  [Andreas Tille]

  * Draft packaging

  [Afif Elghraoui]

  * Finalized packaging

  [Steffen Moeller]

  * Added license text to d/copyright

  * (mostly) fixed narrowing build problem in src/AMOS

  * Does not build because of hash_multimap issue

 -- Afif Elghraoui <afif@ghraoui.name>  Wed, 12 Aug 2015 00:52:14 -0700

	       zlib1g,

	       python,

	       perl

Standards-Version: 3.9.6

Standards-Version: 4.1.3

Homepage: http://amos.sourceforge.net/

Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/amos.git

Vcs-Svn: git://anonscm.debian.org/debian-med/amos.git

Vcs-Browser: https://salsa.debian.org/med-team/amos

Vcs-Git: https://salsa.debian.org/med-team/amos.git

Package: amos-assembler

Architecture: any

Files: debian/*

Copyright: © 2012 Andreas Tille <tille@debian.org>

License: Artistic

License: Artistic

 This program is free software; you can redistribute it and/or modify it

 under the terms of the "Artistic License" which comes with Debian.

 .

 THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED

 WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES

 OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.

 .

 On Debian systems, the complete text of the Artistic License

 can be found in "/usr/share/common-licenses/Artistic".

Index: amos/src/AMOS/utility_AMOS.cc

===================================================================

--- amos.orig/src/AMOS/utility_AMOS.cc

+++ amos/src/AMOS/utility_AMOS.cc

@@ -24,6 +24,8 @@ const char COMPLEMENT_DNA[256] =

      80, 81,'Y','S','A', 85,'B','W','X','R', 90, 91, 92, 93, 94, 95,

      96,'t','v','g','h',101,102,'c','d',105,106,'m',108,'k','n',111,

     112,113,'y','s','a',117,'b','w','x','r',122,123,124,125,126,127,

+/*

+    these are not char values

     128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,

     144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,

     160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,

@@ -32,6 +34,17 @@ const char COMPLEMENT_DNA[256] =

     208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,

     224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,

     240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255

+*/

+    -128, -127, -126, -125, -124, -123, -122, -121, -120, -119, -118,

+    -117, -116, -115, -114, -113, -112, -111, -110, -109, -108, -107,

+    -106, -105, -104, -103, -102, -101, -100, -99, -98, -97, -96, -95,

+    -94, -93, -92, -91, -90, -89, -88, -87, -86, -85, -84, -83, -82,

+    -81, -80, -79, -78, -77, -76, -75, -74, -73, -72, -71, -70, -69,

+    -68, -67, -66, -65, -64, -63, -62, -61, -60, -59, -58, -57, -56,

+    -55, -54, -53, -52, -51, -50, -49, -48, -47, -46, -45, -44, -43,

+    -42, -41, -40, -39, -38, -37, -36, -35, -34, -33, -32, -31, -30,

+    -29, -28, -27, -26, -25, -24, -23, -22, -21, -20, -19, -18, -17,

+    -16, -15, -14, -13, -12, -11, -10, -9, -8, -7, -6, -5, -4, -3, -2, -1

   };

Index: amos/src/AMOS/inttypes_AMOS.hh

===================================================================

--- amos.orig/src/AMOS/inttypes_AMOS.hh

+++ amos/src/AMOS/inttypes_AMOS.hh

@@ -75,8 +75,12 @@ inline uint8_t Char2Qual (char qual)

 //!

 inline std::string Decode (NCode_t ncode)

 {

-  char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX,

-		  ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'};

+  // this is buggy

+  char buff[4];

+  buff[0] = ncode%128;

+  buff[1] = (ncode/256)%128;

+  buff[2] = (ncode/256/256)%128;

+  buff[3] = '\0';

   return buff;

 }

narrowing.patch