while ( $record = Maasha::Biopieces::get_record( $in ) )
{
+ Maasha::Biopieces::put_record( $record, $out );
+
if ( exists $record->{ 'SEQ' } )
{
$gaps = find_gaps( $record->{ 'SEQ' }, $options->{ 'min_len' } );
Maasha::Biopieces::put_record( $gap, $out );
}
}
-
- Maasha::Biopieces::put_record( $record, $out );
}
Maasha::Biopieces::close_stream( $in );
--- /dev/null
+SEQ: NNNNNNNNNNtatcgatcgatcgaacgt
+SEQ_LEN: 28
+SEQ_NAME: test1
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+SEQ: tatcgatcgatcgaacgtnnnnnnnnnn
+SEQ_LEN: 28
+SEQ_NAME: test2
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+SEQ: tatcgatcNNNNNNNNNNgatcgaacgt
+SEQ_LEN: 28
+SEQ_NAME: test3
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+SEQ: NNNNtatcgatcgatcgaacgt
+SEQ_LEN: 22
+SEQ_NAME: test4
+---
+SEQ: tatcgatcgatcgaacgtnnnn
+SEQ_LEN: 22
+SEQ_NAME: test5
+---
+SEQ: tatcgatcNNNNgatcgaacgt
+SEQ_LEN: 22
+SEQ_NAME: test6
+---
--- /dev/null
+SEQ: NNNNNNNNNNtatcgatcgatcgaacgt
+SEQ_NAME: test1
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+SEQ: tatcgatcgatcgaacgtnnnnnnnnnn
+SEQ_NAME: test2
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+SEQ: tatcgatcNNNNNNNNNNgatcgaacgt
+SEQ_NAME: test3
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+SEQ: NNNNtatcgatcgatcgaacgt
+SEQ_NAME: test4
+SEQ_LEN: 22
+---
+SEQ: tatcgatcgatcgaacgtnnnn
+SEQ_NAME: test5
+SEQ_LEN: 22
+---
+SEQ: tatcgatcNNNNgatcgaacgt
+SEQ_NAME: test6
+SEQ_LEN: 22
+---
--- /dev/null
+SEQ: NNNNNNNNNNtatcgatcgatcgaacgt
+SEQ_NAME: test1
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+SEQ: tatcgatcgatcgaacgtnnnnnnnnnn
+SEQ_NAME: test2
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+SEQ: tatcgatcNNNNNNNNNNgatcgaacgt
+SEQ_NAME: test3
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+SEQ: NNNNtatcgatcgatcgaacgt
+SEQ_NAME: test4
+SEQ_LEN: 22
+---
+S_LEN: 4
+S_ID: test4
+S_BEG: 0
+S_END: 3
+---
+SEQ: tatcgatcgatcgaacgtnnnn
+SEQ_NAME: test5
+SEQ_LEN: 22
+---
+S_LEN: 4
+S_ID: test5
+S_BEG: 18
+S_END: 21
+---
+SEQ: tatcgatcNNNNgatcgaacgt
+SEQ_NAME: test6
+SEQ_LEN: 22
+---
+S_LEN: 4
+S_ID: test6
+S_BEG: 8
+S_END: 11
+---
--- /dev/null
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in -m 3 -O $tmp"
+assert_no_diff $tmp $out.2
+clean