version bump

modules/bamutils/best/index.md

@@ -0,0 +1,27 @@
+---
+layout: templ
+title: best
+module: bamutils
+---
+
+    Given a BAM file sorted by read name with potentially multiple mappings, this
+    will remove all but the best mapping.
+
+    The value of the attribute/tag given will be used to determine which reads
+    should be kept and which should be discarded. The tag should be a numeric
+    (int/float) type. Multiple tags may be used. This defaults to 'AS+, NM-'.
+
+
+    Usage: bamutils best {opts} input.bam output.bam
+
+    Options
+      -tag VAL    Tag to use to determine from which file reads will be taken.
+                  (must be type :i or :f) You may have more than one of these,
+                  in which case they will be sorted in order. You can add a +/-
+                  at the end of the name to signify sort order (asc/desc). 
+                  [default: AS+, NM-]
+
+      -fail filename.bam    Write all failed mappings to this file.
+
+
+

modules/bamutils/convertregion/index.md

@@ -36,6 +36,7 @@ module: bamutils
 
     Options:
       -f             Force overwriting an existing out.bam file
+      -unmapped      Keep all unmapped reads in the output file (including invalid junction reads)
 
       -overlap N     Require that all reads must overlap a splice junction
                      by N bases. This also removes unmapped reads. [default 4]

modules/bamutils/index.md

@@ -10,6 +10,7 @@ module: bamutils
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/cims">cims</a></td><td>Finds regions of unusual deletions (CLIP-seq) (experimental)</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/count">count</a></td><td>Calculates counts/FPKM for genes/BED regions/repeats (also CNV)</td></tr>
 <tr><td colspan="3"><h3>General</h3></td></tr>
+<tr><td>&nbsp;</td><td><a href="/modules/bamutils/best">best</a></td><td>Filter out multiple mappings for a read, selecting only the best</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/convertregion">convertregion</a></td><td>Converts region mapping to genomic mapping</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/export">export</a></td><td>Export reads, mapped positions, and other tags</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/expressed">expressed</a></td><td>Finds regions expressed in a BAM file</td></tr>
@@ -19,6 +20,7 @@ module: bamutils
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/keepbest">keepbest</a></td><td>Parses BAM file and keeps the best mapping for reads that have multiple mappings</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/merge">merge</a></td><td>Combine multiple BAM files together (taking best-matches)</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/nearest">nearest</a></td><td>Find the nearest annotated BED region for each read (experimental)</td></tr>
+<tr><td>&nbsp;</td><td><a href="/modules/bamutils/pair">pair</a></td><td>Given two separately mapped paired files, re-pair the files</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/pcrdup">pcrdup</a></td><td>Find and mark PCR duplicates (experimental)</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/peakheight">peakheight</a></td><td>Find the size (max height, width) of given peaks (BED) in a BAM file</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/removeclipping">removeclipping</a></td><td>Postprocesses a BAM file to remove all clipping from reads and alignments (experimental)</td></tr>

modules/bamutils/merge/index.md

@@ -16,22 +16,29 @@ module: bamutils
     the same order as the first file.
 
     The value of the attribute/tag given will be used to determine which reads
-    should be kept and which should be discarded. The tag should be a numberic
-    (int/float) type. This defaults to 'AS'.
+    should be kept and which should be discarded. The tag should be a numeric
+    (int/float) type. More than one tag may be used. This defaults to ['AS+', 'NM-'].
 
-    Additionally, each file can have more than one record for each read, but they
-    should all have the same value for the tag used in determining which reads to
-    keep. For example, if the AS tag is used (default), then each read in a file
-    should have the same AS value. Reads in different files will have different
-    values.
+    Additionally, each file can have more than one record for each read, that may
+    all have the same value for the tag used in determining which reads to keep.
+    For example, if the AS tag is used (default), then each read in a file
+    may have the same AS value. In this case, all reads with the best AS score
+    will be kept.
 
 
 
     Usage: bamutils merge {opts} out.bam in1.bam in2.bam ...
 
     Options
-      -tag VAL    Tag to use to determine from which file reads will be taken
-                  (must be type :i or :f) [default: AS]
+      -tag VAL    Tag to use to determine from which file reads will be taken.
+                  (must be type :i or :f) You may have more than one of these,
+                  in which case they will be sorted in order. You can add a +/-
+                  at the end of the name to signify sort order (asc/desc). 
+                  [default: AS+, NM-]
+
       -discard    Discard reads that aren't mapped in any file.
 
+      -keepall    Keep all mappings for each read, not just the best one.
+                  (Note: only one mapping to each ref/pos will be kept)
+
 

modules/bamutils/pair/index.md

@@ -0,0 +1,47 @@
+---
+layout: templ
+title: pair
+module: bamutils
+---
+
+    Given two separately mapped paired-end files, re-pair the files, selecting
+    the most likely pairing partners based upon strand, insert distance, and
+    maximizing alignment scores.
+
+    It is very important that the files are either in the same order with each
+    read present in both files or sorted in name order.
+
+    The value of the attribute/tag given will be used to determine which reads
+    should be kept and which should be discarded. The tag should be a numeric
+    (int/float) type. More than one tag can be used. The default is 'AS+, NM-'.
+
+    The BEST pair will be kept that maximizes the tag values and otherwise
+    satisfies strand and distance values.
+
+
+    Usage: bamutils pair {opts} out.bam read1.bam read2.bam 
+
+    Options
+      -tag VAL            Tag to use to determine from which file reads will be
+                          taken. (must be type :i or :f) You may have more than
+                          one of these, in which case they will be sorted in
+                          order. You can add a +/- at the end of the name to 
+                          signify sort order (asc/desc). 
+                          Default: AS+, NM-
+
+      -size low-high      The minimum/maximum insert size to accept. By default,
+                          this will attempt to minimize the distance between
+                          reads, upto the lower-bound. Any pair over the upper
+                          bound will be discarded. Note: for RNA, because it is
+                          impossible to detect junctions that are between the
+                          reads, this should be a very big range (ex: 50-1000000)
+                          Default: 50-10000
+
+      -fail1 fname.bam    Write all failed mappings from read1 to this file
+      -fail2 fname.bam    Write all failed mappings from read1 to this file
+                          (Note: -fail1 and -fail2 can be the same file.)
+
+      -reason tag         Write the reason for failure to this tag (only for
+                          failed reads/mappings) Must be a valid two char name.
+
+

modules/bamutils/stats/index.md

@@ -16,6 +16,8 @@ module: bamutils
     Options:
         -all    Show the stats for all fragments (defaults to just the first fragment)
 
+        -nofill Don't fill in missing values when showing stat distributions
+
         -region chrom:start-end
                 Only calculate statistics for this region
 

modules/bamutils/tag/index.md

@@ -12,6 +12,7 @@ module: bamutils
       -orig-ref
       -orig-pos
       -orig-cigar
+      -junction
 
     Usage: bamutils tag {opts} in.bamfile out.bamfile
 
@@ -26,6 +27,8 @@ module: bamutils
 
       -tag tag         Add an arbitrary tag (ex: -tag XX:Z:test)
 
+      -junction tag    Predicts junction spans from CIGAR alignment
+
       -orig-ref tag    Add a new tag with the original reference name (For
                        example, in a region-based BAM will be converted to
                        standard coordinates)

modules/bamutils/tobedgraph/index.md

@@ -4,25 +4,28 @@ title: tobedgraph
 module: bamutils
 ---
 
-    Convert BAM coverage to bedGraph based on pileup counts
+    Convert BAM coverage to bedGraph based on read depth. This will take into
+    account gaps in RNAseq alignments and not display any coverage across introns.
 
-    Takes a BAM file and produces a bedGraph file.  This can optionally
-    normalize the counts by a given factor.
+    This can optionally normalize the counts by a given factor or display only
+    coverage for a specific strand.
 
      See: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
           http://genome.ucsc.edu/goldenPath/help/bigWig.html
 
-    Usage: bamutils tobedgraph [-plus | -minus] {-norm N} bamfile
+    Usage: bamutils tobedgraph {opts} bamfile
 
     Options:
-        -plus             only count reads on the plus strand
+        -plus             Only count reads on the plus strand
                           (default: count all reads)
-        -minus            only count reads on the minus strand
+        -minus            Only count reads on the minus strand
 
-        -norm VAL         the count at every position is calculated as:
+        -norm VAL         The count at every position is calculated as:
                           floor(count * VAL).
 
-        -nogaps           Don't include gaps across splice-junctions (RNA-seq)
-                          Warning: adds significant processing time!
+        -ref name         Only count reads mapping to this reference (chrom)
+
+        -region chr:start-end    Count reads mapping to this genome region
+                                 (start is 1-based)
 
 

modules/fastqutils/filter/index.md

@@ -36,6 +36,7 @@ module: fastqutils
                                   percentage [pct] (0.0-1.0)
 
       -paired                     Only keep reads that are correctly paired
+                                  (Requires an interlaced FASTQ file)
 
       -whitelist keeplist.txt     Only keep reads whose name is in the keeplist
 

modules/fastqutils/properpairs/index.md

@@ -5,10 +5,11 @@ module: fastqutils
 ---
     File -h doesn't exist!
 
-    Usage: fastqutils properpairs filename1.fastq{.gz} filename2.fastq{.gz} output1 output2
+    Usage: fastqutils properpairs {opts} filename1.fastq{.gz} filename2.fastq{.gz} output1 output2
 
     Options:
-      -f    Force overwriting output file (if it exists)
-      -z    Output files should be gzip compressed
+      -f       Force overwriting output file (if it exists)
+      -z       Output files should be gzip compressed
+      -t dir   Use {dir} for temporary files