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#!/usr/bin/env python

############################################
# SAM File Re-organizer
###########################################
#
# what if you took a SAM file and transposed the data, 
# that is, make it so that the rows become columns and vice versa, even keeping 
# optional tags?  Would the file compress better?
#

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diff --git a/src/sw/lib/Solution4.cpp b/src/sw/lib/Solution4.cpp
index 497d71a..f019480 100644
--- a/src/sw/lib/Solution4.cpp
+++ b/src/sw/lib/Solution4.cpp
@@ -1,7 +1,8 @@
 // Coder: Psyho
 // Submission: 40
 // URL: http://community.topcoder.com/longcontest/?module=ViewProblemSolution&pm=11786&rd=15078&cr=10597114&subnum=40
-#define INLINE   __attribute__ ((always_inline))
+//#define INLINE   __attribute__ ((always_inline))

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# tmap mapall -f ${REF} -r r0.fq -v stage1 map1 map2 map3 > r0.fq.map1map2map3.sam
40  84212   0
39  84470   0
38  84724   0
37  85033   0
36  85271   0
35  85438   0
34  85632   0
33  85988   0
32  86200   0

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# tmap mapall -f ${REF} -r r0.fq -v stage1 map1 map2 map3 > r0.fq.map1map2map3.sam
40 77347 0
39 77817 0
38 78306 0
37 78962 0
36 79452 0
35 79794 0
34 80128 0
33 80742 0
32 81118 0

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nilshomer$ ./bin/brew install -v tmap
==> Cloning https://github.com/iontorrent/TMAP.git
git clone --depth 1 --branch tmap.3.2.0 https://github.com/iontorrent/TMAP.git /Users/nilshomer/Library/Caches/Homebrew/tmap--git
Cloning into '/Users/nilshomer/Library/Caches/Homebrew/tmap--git'...
remote: Counting objects: 2272, done.
remote: Compressing objects: 100% (1182/1182), done.
remote: Total 2272 (delta 1681), reused 1564 (delta 1085)
Receiving objects: 100% (2272/2272), 6.20 MiB | 928 KiB/s, done.
Resolving deltas: 100% (1681/1681), done.
warning: Remote branch tmap.3.2.0 not found in upstream origin, using HEAD instead

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      switch (c)
        {
        /* Old McDonald had a farm ei...  */
        case 'e':
        case 'i':
        case 'o':

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enum {
  MISSING_CODE,
  HOM_REF_CODE, 
  HET_REF_VAR1_CODE, 
  HET_VAR1_VAR2_CODE, 
  HOM_VAR1_CODE, 
  NO_CALL_CODE, 
  LOW_GQ_CODE, 
  LOW_DP_CODE, 
  VC_FILTERED_CODE, 

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package picard.sam;

import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloserUtil;

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//  jeanluc/src/main/scala/dagr/jeanluc/JeanLucMain.scala
/*
 * The MIT License
 *
 * Copyright (c) 2016 Fulcrum Genomics LLC
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

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Unit Tests	Integration Tests
Master	GATK	Picard