text: user123: I am mapping kmers back to a few bacterial genomes using bwa fastmap:
  bwa fastmap -l 9 ref.fasta kmers.fasta > out.fastmap                                           
  [M::bwa_idx_load_from_disk] read 0 ALT contigs                                                                                                                                                                     
  [main] Version: 0.7.17-r1188                                                                                                                                                                                       
  [main] CMD: bwa fastmap -l 9 ref.fasta kmers.fasta                                                                                                                   
  [main] Real time: 0.168 sec; CPU: 0.157 sec
  
  The output looks like this:
  SQ      AAAAGTAGTAAGCAGGAAGACAACACGGTTG 31
  EM      0       11      1       contig1:+2041368
  EM      3       13      2       contig1:+1875252        contig1:-2474744
  EM      4       15      1       contig1:+3779779
  EM      5       16      1       contig1:-3253348
  EM      6       17      2       contig1:+938710 contig1:+1066682
  EM      7       20      1       contig1:-4912797
  EM      10      21      4       contig1:+4803473        contig1:-2830252        contig1:+4495150        contig1:-4907283
  EM      11      23      1       contig1:-3148132
  EM      13      24      1       contig1:-4651172
  EM      14      25      3       contig1:-2142223        contig1:+4994474        contig1:+873066
  EM      16      26      4       contig1:+156775 contig1:+27749  contig1:+2207492        contig1:-1340811
  EM      17      29      1       contig1:+3523989
  EM      19      30      24      *
  
  EM      20      31      3       contig1:-2533354        contig1:-208660 contig1:-1080177
  //
  
  My question is: what is the meaning of the * char in the row before last? Why is bwa fastmap not reporting all the hits as in the other lines? I could not find a page that explains this output anywhere.
  
  user-1: It means the read is unmapped. No origin in the reference could be found that was sufficiently similar to the read to call it a proper alignment.
  In the SAM specification, * is always used if the information for that field is not available. Therefore, if no mapping information is available (=unmapped) one sets *. 
  
  user8703: Just starting to work with bwa fastmap and indeed the documentation is very sparse...
  This is what we get from running the program without arguments:
  bwa fastmap
  
  Usage:   bwa fastmap [options] <idxbase> <in.fq>
  
  Options: -l INT    min SMEM length to output [17]
           -w INT    max interval size to find coordiantes [20]
           -i INT    min SMEM interval size [1]
           -L INT    max MEM length [2147483647]
           -I INT    stop if MEM is longer than -l with a size less than INT [0]
  
  Which is a bit cryptic as is...
  The output does not really follow SAM specification and I'm pretty sure the '*' means does not mean unmapped (in fact an unmapped Exact Match doesn't make any sense does it?)
  In fact, the '*' means that there are too many matches to print the reference id and position.
  Looking quickly into the source code this is controlled by the -w arguments.
  It defaults to 20, which is why you don't get an output for your 24 matches.
  
original_text: 123: <p>I am mapping kmers back to a few bacterial genomes using <code>bwa fastmap</code>:</p>
  
  <pre><code>bwa fastmap -l 9 ref.fasta kmers.fasta &gt; out.fastmap                                           
  [M::bwa_idx_load_from_disk] read 0 ALT contigs                                                                                                                                                                     
  [main] Version: 0.7.17-r1188                                                                                                                                                                                       
  [main] CMD: bwa fastmap -l 9 ref.fasta kmers.fasta                                                                                                                   
  [main] Real time: 0.168 sec; CPU: 0.157 sec
  </code></pre>
  
  <p>The output looks like this:</p>
  
  <pre><code>SQ      AAAAGTAGTAAGCAGGAAGACAACACGGTTG 31
  EM      0       11      1       contig1:+2041368
  EM      3       13      2       contig1:+1875252        contig1:-2474744
  EM      4       15      1       contig1:+3779779
  EM      5       16      1       contig1:-3253348
  EM      6       17      2       contig1:+938710 contig1:+1066682
  EM      7       20      1       contig1:-4912797
  EM      10      21      4       contig1:+4803473        contig1:-2830252        contig1:+4495150        contig1:-4907283
  EM      11      23      1       contig1:-3148132
  EM      13      24      1       contig1:-4651172
  EM      14      25      3       contig1:-2142223        contig1:+4994474        contig1:+873066
  EM      16      26      4       contig1:+156775 contig1:+27749  contig1:+2207492        contig1:-1340811
  EM      17      29      1       contig1:+3523989
  EM      19      30      24      *
  
  EM      20      31      3       contig1:-2533354        contig1:-208660 contig1:-1080177
  //
  </code></pre>
  
  <p>My question is: what is the meaning of the <code>*</code> char in the row before last? Why is <code>bwa fastmap</code> not reporting all the hits as in the other lines? I could not find a page that explains this output anywhere.</p>
   -1: <p>It means the read is unmapped. No origin in the reference could be found that was sufficiently similar to the read to call it a proper alignment.</p>
  
  <p>In the <a href="http://samtools.github.io/hts-specs/SAMv1.pdf" rel="nofollow noreferrer">SAM specification</a>, <code>*</code> is always used if the information for that field is not available. Therefore, if no mapping information is available (=unmapped) one sets <code>*</code>. </p>
   8703: <p>Just starting to work with bwa fastmap and indeed the documentation is very sparse...
  This is what we get from running the program without arguments:</p>
  
  <pre><code>bwa fastmap
  
  Usage:   bwa fastmap [options] &lt;idxbase&gt; &lt;in.fq&gt;
  
  Options: -l INT    min SMEM length to output [17]
           -w INT    max interval size to find coordiantes [20]
           -i INT    min SMEM interval size [1]
           -L INT    max MEM length [2147483647]
           -I INT    stop if MEM is longer than -l with a size less than INT [0]
  </code></pre>
  
  <p>Which is a bit cryptic as is...</p>
  
  <p>The output does not really follow SAM specification and I'm pretty sure the '*' means does not mean unmapped (in fact an unmapped Exact Match doesn't make any sense does it?)</p>
  
  <p>In fact, the '*' means that there are too many matches to print the reference id and position.
  Looking quickly into the source code this is controlled by the -w arguments.</p>
  
  <p>It defaults to 20, which is why you don't get an output for your 24 matches.</p>
  