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* mate is unmapped
* mate is unmapped
* secondary alignment (not primary alignment)
* secondary alignment (not primary alignment)
* supplementary alignment
* duplicates
* duplicates
* QC Failure
* QC Failure
= Usage =
= Usage =
./bam gapInfo --in <inputFile> --out <outputFile> [--noeof] [--params]
./bam gapInfo --in <inputFile> --out <outputFile> [--noeof] [--params]
= Parameters =
= Parameters =
--out : the output file to be written
--out : the output file to be written
Optional Parameters:
Optional Parameters:
--refFile : reference file, used to skip gaps that include reference base 'N' (for runs without --detailed)
--refFile : reference file, used to skip gaps that include reference base 'N' (for runs without --detailed) --detailed : Print the details for each read pair
Optional Parameters for the Detailed Option:
Optional Parameters for the Detailed Option:
--checkFirst : Check the first in pair flag and print "NotFirst" if it isn't first
--checkFirst : Check the first in pair flag and print "NotFirst" if it isn't first
--noeof : Do not expect an EOF block on a bam file.
--noeof : Do not expect an EOF block on a bam file.
--params : Print the parameter settings to stderr
--params : Print the parameter settings to stderr
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{{PhoneHomeParamDesc}}
== Required Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile}}
== Output File (<code>--out</code>) ==
=== Output File (<code>--out</code>) ===
Use <code>--out</code> followed by a file name to specify the output file to write.
Use <code>--out</code> followed by a file name to specify the output file to write.
Detailed output does not have a header line and is described below under the [[#Print Detailed Per-Pair Information (<code>--detailed</code>) | --detailed]] parameter.
Detailed output does not have a header line and is described below under the [[#Print Detailed Per-Pair Information (<code>--detailed</code>) | --detailed]] parameter.
== Optional Prameters ==
{{RefFile}}
{{RefFile}}
With this option specified, do not increment counters for the number of times that a gap is found if any of the reference bases in the gap are an 'N'. (N/A if <code>--detailed</code> is specified.)
With this option specified, do not increment counters for the number of times that a gap is found if any of the reference bases in the gap are an 'N'. (N/A if <code>--detailed</code> is specified.)
== Print Detailed Per-Pair Information (<code>--detailed</code>) ==
=== Print Detailed Per-Pair Information (<code>--detailed</code>) ===
With this option, for every record processed per the above rules, the following information is printed on a line as tab separated columns:
With this option, for every record processed per the above rules, the following information is printed on a line as tab separated columns:
* Reference/Chromosome Name
* Reference/Chromosome Name
Detailed output does not have a header line.
Detailed output does not have a header line.
== (<code>--checkFirst</code>) ==
See [[#Optional Parameters for --detailed|Optional Parameters for <code>--detailed</code>]] for additional options related to <code>--detailed</code>.
Only applicable if <code>--detailed</code> is also provided.
{{noeofBGZFParameter}}
{{paramsParameter}}
== Optional Parameters for [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] ==
=== Check First (<code>--checkFirst</code>) ===
Only applicable if [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided.
When specified along with <code>--detailed</code>, the output for each record processed also includes "NotFirst" if it is not marked as FirstFragment in the flags.
When specified along with [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "NotFirst" if it is not marked as FirstFragment in the flags.
== (<code>--checkStrand</code>) ==
=== Check Strand (<code>--checkStrand</code>) ===
Only applicable if <code>--detailed</code> is also provided.
Only applicable if [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided.
When specified along with <code>--detailed</code>, the output for each record processed also includes "Reverse" if it is marked as the reverse strand in the flags.
When specified along with [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "Reverse" if it is marked as the reverse strand in the flags.
{{noeofBGZFParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
Returns -1 if input parameters are invalid.
Returns -1 if input parameters are invalid.
Returns the SamStatus for the reads/writes (0 on success).
Returns the SamStatus for the reads/writes (0 on success, non-0 on failure).
= Output =
= Output =
